Having lost 1-0 in the first leg at Eastlands earlier this month, City knew the size of the task ahead in their second qualifying round return leg at the SAS Arena in Herning.
But after an abject display in normal time it was only an own goal by defender Danny Califf in the 89th minute which forced extra-time and extended their interest in the competition.
And when Hart saved two penalties in the shoot-out, it was left to Vedran Corluka to stroke home the kick to spare City's blushes.
City, who reached the preliminary stages by virtue of their position in last season's Fair Play league, had faced a stern test against a well-organised and dynamic counter-attacking Danish side and were clearly the poorer of the two teams for the majority of the game.
They were boosted before kick-off by Micah Richards' rapid recovery from concussion and also by the signing of Shaun Wright-Phillips from Chelsea.
A sixth-minute Elano corner was only partially cleared, allowing Martin Petrov to hook the ball back into the area but Stephen Ireland fired wide on the half-volley as City looked to score the early goal.
Barely a minute later they needed goalkeeper Hart to keep the tie alive however. When Jonas Borring beat the offside trap he looked set to double his side's aggregate lead, only for the England Under-21 international to make a smart save.
While Jo , back from the Olympics, and Elano saw speculative shots fail miserably Borring, the Danes' chief playmaker, was proving to be more effective and had another well-struck shot comfortably saved by Hart.
First-leg goalscorer Danny Olsen had the best chance of the match up to that point when he moved to side-foot home Borring's low centre in the 28th minute, only to be denied by an excellent sliding block by left-back Michael Ball.
City continued to labour, devoid of creative ideas, until Jo headed out to the left flank and forced Midtjylland to scramble his cross clear, while Petrov fired in an effort from an acute angle which Lasse Heinze got down well to save two minutes before the break.
City won a corner early in the second half when Jo was beaten to a header and from the resulting set-piece, Richards' header was blocked before Petrov's shot was similarly turned away.
Hughes sent on Dietmar Hamann and Daniel Sturridge for Tal Ben-Haim and Elano shortly before the hour mark with Richards moving into central defence.
Hart was forced into action to clear the danger on the edge of his area after Mikkel Thygesen found himself through on goal beyond the flat-footed City defence.
Midtjylland boss Thomas Thomasberg sent on young striker Collins Babatunde for Jude Ikechukwu Nworuh.
Substitute Collins almost made an immediate impact with a glanced header but saw his effort fly narrowly wide of the far post only for two more dangerous chances to also go to waste.
Richards was booked for an innocuous-looking challenge before Claus Madsen was introduced by the home team.
Ched Evans was sent on for the ineffective Jo and soon had an impact. The goal City craved so desperately came from nothing in the 89th minute when Evans failed to properly connect with Ball's cross and the ball was deflected past despairing goalkeeper Heinze by defender Califf.
Extra-time began without incident until the 96th minute, when Sturridge expertly put Michael Johnson through on goal only for the midfielder to see his effort saved by the advancing Heinze. When the ball was crossed back into the area, Ireland could not head on target.
Sturridge was looking lively and struck the bar in the 103rd minute after receiving the ball on the right following Hamann's brilliant tackle outside the Midtjylland area.
In the second half Gheorge Florescu struck a powerful shot but Hart got down to hold on to the ball while Johnson fired just wide five minutes later.
Hart was forced to tip the ball over the bar when substitute Frank Kristensen shot on the turn in the 117th minute but penalties beckoned when neither side produced a winning goal.
Evans took the first penalty and scored while Petrov converted his but after Winston Reid and Christopher Poulsen also scored, Johnson saw Heinze dive to save his spot-kick.
Borring also saw his saved, however, before Hamann's kick beat the goalkeeper.
Hart then gave his side the advantage when Kolja Afriyie had his kick saved and Corluka converted his kick to send Hughes' side through.
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bluemoon risin' (28/08/2008 at 18:25)
Well we dont know where were goin
But we know where weve been
And we know what were knowin'
But we can't say, what we've not seen
And we cry like little children
On this forum, what do we want?
And the future is certain?
Give frank time to, work it out
We're on the road to europe, sing it with pride
Taken that road to groclin
bumpy old ride
Im feelin okay this morning
And you know,
We've won the game in midgetland
Here we go, here we go
Chorus
Maybe a drink in some icelandic bar
I dont care
We'll raise a glass and sing with pride
See you there...see you there
Were on a road to europe, yeah
Were on a road to europe, yeah
Were on a road to europe, yeah
Theres man city in my mind
Come along and take that ride
And its all right, buddy, its all right
And the final's far away
Its in istanbul next may
If its blue and white, book me on that flight !
Would you like to come along, and help me sing this song
its alright, baby its alright.
There'll be thousands, shirts of blue
Drinking efes ,,,,,, raki too
And its all right, buddy, what a nite
We've been on the road to nowhere
lincoln and wycombe, been there!
Were on a road to europe, yeah!
Were on a road to,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, europe, Yeh!
Great result lads. Come on city!
mufc who else (28/08/2008 at 18:26)
Wait till a gun guns team comes along.
Qas (28/08/2008 at 18:26)
Hart was a hero.
Al, Buxton, Buxton (28/08/2008 at 18:27)
Ooh Vonky Vonky.., Offerton (28/08/2008 at 18:29)
Alves the Ninja, Sheffield (28/08/2008 at 18:30)
Lambadonna (28/08/2008 at 18:31)
Bluemonster, Mossley (28/08/2008 at 18:31)
Niall Quinn's Disco Pants, Ashton (28/08/2008 at 18:32)
True Blue Middlesbrough, middlesbrough (28/08/2008 at 18:32)
Phil, Sacramento, CA U.S.A. (28/08/2008 at 18:33)
NYC Blue (28/08/2008 at 18:33)
"yozzer" hughes, manchester (28/08/2008 at 18:33)
bluemoon risin' (28/08/2008 at 18:34)
He's amazing,he's blue he's in goal, he's joe hart.
Have you seen him, capello,
he can light up the dark.
try as i may, i can never complain,
What you'll see soon, is englands no1 king.
[chorus]
He'l put fear on your face,
Cos he's big,, over 6-3.
He's had plenty of pies,
since we signed him, from shrewsbury!
The size of his hands, are like big cornish pasties
and they hide the ball !
When joe at his best.
Then u'll score nothin at all !
When joe at his best.
Then u'll score nothin at all !
When joe at his best.
Then u'll score nothin at all !
Englands number one.
Great saves joe.
Bluemoon (28/08/2008 at 18:39)
Evans penalty was great!!!
sigmund fraud (28/08/2008 at 18:41)
Jack Thorley Trafford, Timperley (28/08/2008 at 18:42)
SUPER CITY OF RAIN MODE (28/08/2008 at 18:44)
(Sam Haggar)Mark Hughes get City to Europe (28/08/2008 at 18:46)
Ooh Vonky Vonky.., Offerton (28/08/2008 at 18:46)
Lambadonna (28/08/2008 at 18:47)
Ste, Cheshire (28/08/2008 at 18:48)
We need to improve dramatically if we are to progress any further.
For me Jo and Elano up front was just a disaster. Jo really needs to do more than that to justify his ridiculous fee. Evans changed it when he came on and he and Sturridge looked very dangerous. I would start with Sturridge again against Sunderland as he and Elano looked much better together. Jo needs easing in and needs to train with the rest of the squad for a week or so before starting against Chelsea.
Where was the urgency? Micah at holding midfield didn't work and Johnson was just lost in that midfield. I didnt think he was playing at one point. Ireland whilst working hard is so infuriating! Excellent against the hammers but not today! What was he doing when clean through with two city players waiting for the cross at the back post? Terrible cut back.
Hammann should have started as he just calms us down and breaks up the play.
Overall very lucky but thats two wins on the bounce now.
Looked like a good day out for the fans! We now need to at least fill the bottom tier for the next game. anything less than 30,000 is just embarrassing!
madMental, Macclesfield (28/08/2008 at 18:50)
trueblue, manchester (28/08/2008 at 18:51)
Neville Nevilles ugliest son phil (28/08/2008 at 18:53)