The robust striker was in the right place at the right time to nod home a loose ball from a corner and claim his 17th goal of the season, cancelling out Martyn Woolford's opener for the home side.
It was the least the Dons, who finished third in the League One table, deserved for their efforts at Glanford Park. They were the most composed and dangerous side throughout, despite some belated Scunthorpe pressure as the game wore on.
The visitors finished the regular season 11 points clear of the Iron and that was evident for large parts of the tie as they enjoyed the better of the possession and, in wingers Jason Puncheon and Mark Wright, had the brightest performers.
The Dons signalled their intent in the opening minute when Peter Leven got the ball rolling with a drilled effort that warmed up Joe Murphy and, although Scunthorpe's top scorer Gary Hooper should have done better when trying to chip Willy Gueret after breaking through, they enjoyed the better of the early exchanges.
That was soon undone, though, as Scunthorpe took the lead through Woolford's sixth goal of the season. There was little danger when Paul Hayes cut in from the left but, after Gueret could only parry his drive, Woolford did well to bundle the loose ball home with his heel.
To their credit the Dons refused to break from their stride and Puncheon nearly got them back on terms when he crept in at the far post following a Wright cross, before they got the goal their approach play deserved with 27 minutes gone.
Grant McCann needlessly conceded a corner and, after Wright's centre was poorly cleared by Cliff Byrne, Jude Stirling nodded the ball back in and Wilbraham pounced from almost under the crossbar to score.
McCann then wasted two good chances to work Gueret with free-kicks from the edge of the area but the Dons remained the more threatening side going into the interval.
That continued into the second half as Puncheon and Wilbraham both flashed efforts over although Scunthorpe remained dangerous on the break and Hooper had a goal disallowed for offside as he bundled home Hayes' shot at the back post following a mistake from Luke Howell.
The chances continued to present themselves to the visitors and Miguel Angel Llera should have done better than head over from Wright's corner when completely unmarked, while Wright himself blazed wide after Wilbraham's cute back-heel had played him in.
Hayes and Krystian Pearce then went close for Scunthorpe, with Stirling excellent in blocking the latter's shot, before the finest chance fell to Dons substitute Sam Baldock. He did the hard work in rounding Murphy but then picked out the legs of the covering David Mirfin rather than the open goal.