Things looked good early on for the Dons as they took their superb form from the 5-1 thrashing of Bury into this game and dominated the first half with some pacy attacking football.
It was aided by the fact they got an early goal through Gallen.
Keith Andrews split the defence with a perfect throughball to the experienced striker who held off his marker well and stroked the ball into the far corner of the net after 14 minutes.
In reply the dangerous Brogan had two efforts from the edge of the box but hit both at Willy Gueret.
The Dons could have doubled their lead on the half-hour mark when Alan Navarro played a delightful chipped ball over the defence for Lloyd Dyer who just beat the keeper to the ball, but couldn't beat the covering Adrian Pettigrew who cleared off the line on his Rotherham debut.
Moments later Dyer caused more problems when he beat Pettigrew and squared for Mark Wright but his weak shot was cleared by a Rotherham defender.
But for all the Dons' pressure, the Millers could have levelled on 36 minutes when Chris O'Grady beat a man and unleashed a pile-driver of a shot from 30 yards that was just tipped over by Gueret.
Rotherham were handed a cruel blow in the opening minutes of the second half as their best player, Brogan, was carried off.
The young winger tried to capitalise on some indecision in the Dons defence but Gueret just beat him to the ball, but clattered straight into him feet first.
The game was held up for over five minutes before he left the field to a rapturous applause by both sets of fans.
The loss seemed to sap the life out of the game as neither team looked threatening. The only real effort of note in the 20 minutes afterwards came from Dean Lewington, but his thunderous shot was beaten away by Andy Warrington.
He was made to rue that miss as Harrison (right) punished the Dons with a superb finish on 82 minutes.
Ryan Taylor laid the ball back to him on the edge of the box and his first-time shot whistled into the top corner.
Seven minutes of stoppage time was added but the Dons struggled to create any chances. Harrison could have won the game but his shot from the edge of the box was superbly saved by Gueret at the death.