Trotter who is set to hold talks with Town boss Roy Keane on his future in the near future, was named on the bench for the home side and remained there for the full 90 minutes.
Scunthorpe drew first blood when winger Martyn Woolford found the net after a shot from Paul Hayes had been only half blocked by goalkeeper Willy Gueret.
MK Dons forced their way back on to level terms with their first real effort of the game when striker Aaron Wilbraham squeezed a close range header into the roof of the net after Scunthorpe had failed to clear a corner.
Scunthorpe thought they had gone back in front on the hour when Hooper netted from close range, only to be denied by a linesman's flag for offside.
Home striker Hayes had a shot well turned away by Gueret and from the corner that followed the French keeper excelled again, somehow keeping out a shot from substitute Krystian Pearce from point blank range.
But in the final minutes it was MK Dons who nearly snatched a winner when first Wilbraham saw his goalbound shot blocked away by defender David Mirfin and then substitute Sam Baldock was denied by a last gasp save from keeper Joe Murphy who minutes later, had to hobble off with a recurrence of groin trouble.
The second leg of the Play-Off Semi Final takes places at Stadium MK on Friday 15th May at 7.45pm.
Click here for a rundown of Liam Trotter's season to date.