Blues lost defender Steve Vickers with a foot injury and were then undone by Hughes' skill, whose rising 80th-minute shot gave goalkeeper Ian Bennett no chance, and Agyemang's late goal secured the Don's victory.
Wimbledon's slick passing game meant they had the better of the first half.
Damien Francis had two early chances, first being played in on the left side of the area by David Connolly's pass but Francis slipped as he went to shoot.
Good work by Connolly on the edge of the Blues area again set up Francis, but he shot wide across goal from 20 yards.
Blues then carved out the best chance of the half but were denied by Kelvin Davies in the Wimbledon goal.
His shot was flicked on by Hughes straight into the arms of Davies.
Mooney then set up a good Blues move in the 61st minute when his pass sent Horsfield racing clear.
The "Horse" was felled as Jermaine Darlington and Trond Andersen closed in on him only for Mooney to blaze the spot-kick high over the bar.
As the game looked to be heading for a draw Hughes broke the deadlock with an un-stoppable 30-yard left-foot shot in the 80th minute.
Horsfield then had a chance to level the scores from eight yards out when Lazaridis picked him out in the box with a clever flighted ball but he hurriedly volleyed wide across goal with the inside of his right foot.
Agyemang wrapped up the points in stoppage time with a low shot from just inside the area which went under Bennett and into the net.
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