Dons midfielder Stacy Long smashed a stoppage time penalty winner just seconds after Torquay top scorer Rene Howe had levelled with a last-minute header, his 11th goal of the season.
Paul McCallum got the Dons off to a flyer with his sixth minute headed opener, cancelled out by Lee Mansell's close-range reply two minutes later.
Visiting skipper Mat Mitchell-King restored the Dons advantage with a 33rd minute angled drive before the late drama.
"We are doing exactly the same this season as we did last season, but we didn't concede late goals last season," he said.
"Obviously some of the players have changed but we don't do anything different in training.
"It's to do with mentality and when it happens once, and then twice it's in the back of the players' minds. It's the same with getting out of jail with a late goal.
"But we got out of jail with a late goal here and we still managed to throw it away - and that wasn't happening last season.
"Last season we overachieved to get into the play-offs but this year we are underachieving and of course it's frustrating.
"Maybe we thought we could roll them over because of where Wimbledon are in the table, but there are no games like that. It's never easy and the worst thing you can ever think going into a match is that you are nailed-on to win."