While Swede Robert Karlsson took another step towards the Order of Merit title with an opening three under par 69 - four behind Welshman Stuart Manley - Wilson's hopes of taking a huge leap towards a US Masters debut next April were dashed by a neck injury.
"I woke up with it," said the Mansfield golfer, who had won the eve-of-tournament pro-am.
"I went to get out of bed and felt it go. "I had some physio, took some pills, but when I went to the range to warm up I could only swing it about threequarters at best.
"Normally it loosens up reasonably quickly, but I couldn't reach a couple of holes and it was pointless really."
He had already fallen to four over when he decided to call it a day.
Wilson wants to be in the world's top 50 at the end of the year to secure a first appearance at Augusta, but on Monday he slipped to 51st in the new rankings - 0.001 points behind American Brandt Snedeker.
Manley was a Walker Cup hero in 2003, but has had to make four trips to the Tour school since then and is labouring down in 174th on the money list with two events to go.
"I need some money," said the 29-year-old, who has missed the halfway cut in 20 of his 30 events and has to climb into the top 115 to avoid a return to qualifying.
"It's a good time to find form. I've been fantastic in practice, so it must be a mental issue somewhere.
Bumpy
"The greens were a bit bumpy (he was in the penultimate group of the day), but for some reason the putts went in."
With efforts from 30, 10 and 20 feet be birdied three of his last four to relegate England's Mark Foster, Indian Jyoti Randhawa and big-hitting Spaniard Alvaro Quiros into second place.
Karlsson, £112,000 ahead of Padraig Harrington at the top of the Order of Merit, has a chance to more than quadruple that lead with the Open and US PGA champion having chosen to go to Bermuda instead this week for the Grand Slam of Golf.
With no Harrington - he lost a play-off to Jim Furyk - the 39-year-old Swede was paired instead with Lee Westwood and Miguel Angel Jimenez, third and fourth in the table, and they managed only 72 and 73 respectively.
"I played like a tired man that wants the year to end," stated Westwood, who described his decision to go for the green in two on the long 17th as "amateurish."
He found the lake, then three-putted for a double bogey seven.
"It was not a good lie and I should have laid up," he said of the 246-yard shot.
The trio were followed by an official in a buggy for a while because they fell behind the group in front and Westwood added: "He could have given me a ride, my legs were that bad."
Karlsson, winner of his last two events and runner-up to Steve Webster in last year's Portugal Masters on the same Oceanico Victoria course, is not immune from fatigue himself.
"You definitely know you have flown all over the world for 10 months, but that was not too bad," said the 39-year-old, who made up for four bogeys with seven birdies.
Playing partners Darren Clarke and Colin Montgomerie had 10 birdies between them, but there were nine bogeys and in Clarke's case a double bogey as well. They finished on 72 and 73 respectively.
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