Helder Postiga was on target in his first 90-minute stint since a hamstring injury in the FA Cup tie against Manchester City.
He levelled up Wimbledon's opener at the National Hockey Stadium in Milton Keynes and then won a penalty that Jamie Redknapp drilled home to secure the points in the second half.
Jamie completed another 90 minutes on his road back from injury and was joined in central midfield in the second half by Academy first year Jamie O'Hara, just 17, whose confidence on the ball and intelligent passing caught the eye again.
"Wimbledon were a spirited side, we knew what we were going to be up against and it took us a while to impose ourselves," said coach Clive.
"Once we did and got in front I felt we controlled it and played well. It took a little while for that to happen. There were some good performances again, the two centre-backs were excellent and overall it was a good victory.
"It can be difficult coming back into reserve team football but Helder did well.
"He made some good runs and was a bit unfortunate the final pass didn't find him. He took his goal well. We know he can finish and given opportunities, he will score goals.
"Jamie O'Hara has a lovely touch and has a nice awareness of the game. He's happy to accept the ball in tight areas and he gave us another option in there.
"He doesn't hide, he has an excellent left foot and a good range of passes. He did well."
Clive Allen had plenty of positives to report after Tuesday night's reserve team win against Wimbledon.