The in-form striker hit back with a superb header after former Dons striker Clive Platt had put Colchester United ahead.
The game brought the surprise return of Jason Puncheon on loan, but the tricky winger who won eight out of the nine games he played for the club earlier in the season, was sent off for a lunge on Dean Hammond on the hour mark.
The Dons had been poor before that, but somehow managed to up their game after going down to ten men, Wilbraham heading home superbly from a corner just four minutes later.
The home side were simply lacklustre and outfought by a team who wanted it more in the first half.
They created one chance early on, with Peter Leven just miscuing Jemal Johnson's cross past the post, but they barely had another effort on goal.
The ease with which the visitors took the lead showed the lack of zip in the home team. Mark Yeates was afforded way too much space down the left, he used a bit of trickery to gain half a yard and chipped in a cross that Platt delicately flicked in past the helpless Willy Gueret.
The Dons had plenty of the ball down the left with Johnson but he never managed to find an end product and Sam Baldock let fire with a 30-yard thunderbolt that just fizzed over.
Dons were dealt a blow five minutes before the break when influential midfielder Leven limped off injured, Mark Wright replacing him.
But Colchester could have gone in 2-0 up at the break after Dons failed to clear a corner and the ball was laid off to David Perkins on the edge of the box, who had a left-foot shot well saved by Gueret.
The second half saw a slight up in tempo from Roberto Di Matteo's men, but they still looked short on ideas.
The Cowshed showed how much they were looking for a break when it optimistically appealed for a penalty when Baldock lost out in an aerial collision in the box.
Then just past the hour Puncheon was sent off. He went in rashly on Hammond and referee Anthony Taylor couldn't have had the card out any quicker.
Now without Leven and Puncheon, the Dons looked doomed, but surprisingly it was the thing they needed to spur them on and four minutes later they equalised.
Wilbraham headed in superbly at the far post from Johnson's corner.
You are always vulnerable after you have just scored though and seconds later Yeates was put through on goal, but poked his shot just wide.
Then an error almost let the U's in again as Miguel Llera let a simple ball into the box roll under his foot.
Scott Vernon couldn't have asked for an easier chance with the goal at his mercy from eight yards, but somehow Sean O'Hanlon got a leg in the way to stop a certain goal.
Then in added-on time Colchester should have won the game after good work from substitute Anthony Wordsworth, he laid the ball off for Steven Gillespie who from just eight yards out spooned his effort agonisingly wide of the post.