The Rebels had to wait until the dying seconds of injury-time before centre-half Adam Turner looped in a header from Adam Carden's cross to secure their passage into the second qualifying-round.
The win was no more than FC deserved, as they dominated throughout and only once had cause to panic when Carden denied Steve Howson with a goal-line clearance.
Marginson, an FA Trophy winner as a player with Macclesfield 12 years ago, said: "I'm really proud of the patience and belief we showed. The goal was a long time coming, but I'd say the result was spot-on.
"To get to Wembley would mean everything, but that's a million miles away. All we're now concentrating on is Wednesday's league game at Frickley."
Ashton United and Leigh joined FC in successfully negotiating their opening Trophy hurdle. Goals by Robbie Talbot and skipper Ian Kearney ensured Ashton saw off visiting Lincoln 2-1, while Genesis squeezed past Harrogate Railway courtesy of Jordan Stephen's 20th minute header.
Elsewhere, there was Trophy heartache for Trafford as they fell 3-2 at Whitby, while Witton went out 1-0 at home to Worksop and Salford were hit for six at Stourbridge.
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Free Red, Manchester (21/10/2008 at 12:38)
"The 'Boro' were knocked out of the FA Trophy in controversial circumstances at FC United on Saturday and left club officials questioning the strength and experience of the referee and especially his added time of just short of five minutes, club officials had already been to see the referee at half time in relation to his handling of the game and were stunned when five minutes of added time was used after the board showed three minutes which was also in question, Director of Football Gerry Luczka spoke for all the club and said, "We had questioned the referees handling of the game at half time and it got no better, a lot of frightened decisions were made, we also asked why three minutes were added on and he said he had only played 30 seconds over the three minutes and had spoken to Phil regarding it, having spoken to Phil he had no contact with the ref and when we questioned him again on that he stated he had played four and then changed that to five minutes extra and that was in front of an assessor which was embarrassing. Five minutes was ridiculous and I think everyone knew that I think the referee knew it in the end and to blow when they scored was a real blow for the lads and a terrible decision, If he looked at the dvd of the game he would be able to see himself even three minutes was out of order. I think his reaction and manner after the game said it all really."
"The 'Boro' had defended excellently and deserved a replay based on that defensive display and it looked like their game plan had worked, whilst FC had possession they never really created enough clear cut chances and a draw seemed the right result." It was a terrific performance from the back lads and Phil, in all honesty from there we struggled offensively, we have one or two attacking players that are not at their best at the moment and struggling to find some form and we never caused them enough problems in an attacking sense. The defensive display was focused, disciplined and controlled and deserved a replay for that alone which we should have had. We have to be patient with some players at the moment and stick by them and show them some support, however we need to look at bringing in a couple of players who would make such a difference to the team." said Luczka
Missing were Gary Sampson, Adam Roscoe and Martyn Forrest and Luczka said, "All three would have a different impact on the team and with two players we have already identified which are a forward and midfield player all five would make us a lot stronger, we need to make those movements finance permitting as soon as we can. We spoke about what the merits of a result were yesterday and also about the league situation and the two were fully identified. We have another cup game on Tuesday our third on the bounce and hopefully we can get it out of our system and be better offensively to match our defensive display. I am sure we will not have a hangover no matter how disappointing it ended"