Danny Schofield's early opener was cancelled out by Aaron Wilbraham but Harris bagged a second-half double to hand Kenny Jackett's men their sixth win in seven games.
Harris was denied when one-on-one by Dons keeper Willy Gueret following Peter Leven's poor back-header before Schofield put Millwall ahead in the 19th minute. Schofield jinked his way to the edge of the box and exquisitely curled home his seventh goal of season.
Harris dragged another good chance wide and Gueret saved well from Steve Morison before Wilbraham equalised for the Dons eight minutes after the break. Wilbraham's 25-yard shot took a wicked deflection off Paul Robinson and looped into the corner of the net for his first league goal at stadium:mk since October.
But Harris restored Millwall's lead eight minutes later when he bundled the ball in from a yard, after Chris Hackett's free-kick had caused chaos in the Dons' defence.
And Harris wrapped up the win five minutes from the end when he drilled in his 16th goal of the season after his initial header from substitute Scott Barron's corner had been blocked.