Varney header gives Town a winning end to home season
The striker got on the end of Myles Kenlock’s excellent delivery to power a header into the roof of the net.
David McGoldrick put Blues in front on 15 minutes but then conceded a penalty on the stroke of half-time, Alex Revell scoring from the spot.
Brett Pitman put Town back in front soon after coming on before Revell levelled things up again with a volley from close range.
It looked to have given MK Dons a point until Varney’s header ended Town run of seven games without a win.
Dean Gerken made his first appearance since sustaining a shoulder injury at Birmingham in January, with Kenlock and Josh Emmanuel also coming in as Mick McCarthy changed things up for the last home game of the season.
Dean Bowditch started for the visitors in his first return since leaving Portman Road in 2009.
Kenlock was inches away from opening the scoring with a terrific header from 15 yards, Liam Feeney then whipping in a cross that was aimed at Freddie Sears until Kevin Long read the danger.
McGoldrick, watched by Republic of Ireland boss Martin O’Neill, was denied as he looked to weave his way to goal but on 15 minutes he escaped his marker to volley Sears’ cross into the net.
Dons had a lucky escape when ‘keeper Charlie Burns scuffed his clearance but Karl Robinson’s side played their way out of danger and it needed Christophe Berra to clear after an excellent run from George Baldock.
Burns atoned in style, first saving low to his right from McGoldrick, then clawing away a follow up strike from Teddy Bishop, who was making his first appearance of the season at Portman Road after recovering from a hamstring tendon problem.
Daniel Powell let fly after a good run but Gerken was untroubled, Josh Murphy led a break from a Town free-kick but again Blues’ ‘keeper was able to watch the shot go by.
Berra headed wide from Kevin Bru’s corner, Murphy sending a cross behind the Town defence but away from danger at the other end.
Dons levelled right on half-time, McGoldrick catching Murphy inside the box and Revell made no mistake from the spot-kick.
Bishop burst into the box in the opening minute of the second-half, Long clearing, then McGoldrick deflected a Murphy free-kick just wide.
Gerken beat out Samir Carruthers’ strike, Bishop then just wide with a right foot effort before being replaced by Brett Pitman just past the hour.
It was the striker who headed in from Bru’s free-kick seven minutes after coming on to put Town back in front, Bru then sending a right foot curler just wide.
Varney replaced Feeney in Town’s second change, Bowditch given warm applause from the Blue Army as he made way for Nicky Maynard.
Bru sent a right foot effort high and wide, Kenlock a curler over the bar from the angle of the box before Varney won it with that late header.