The doomed Gloucestershire side went ahead against the run of play when Durrell Berry’s low shot went in off the post.
But Dons earned a point when Jack Smith bravely headed home an equaliser following good work from Alfie Potter and Adebayo Akinfenwa.
Akinfenwa marked the goal by holding up a shirt bearing the name of Sammy Moore’s late mother as the midfielder returned to the squad on the final day.
Wimbledon manager Neal Ardley said: "We could have won by four but we drew 1-1, so that sums up our season.
"There's a lot right with what we're doing; we attack teams, the way we create chances is brilliant- how many chances that get created against us is low.
"We're a very, very good team, but we've been short of a few things.
“There's been a lot of things in my recruitment that I've got wrong during the second half of the season that probably cost us.
“It wasn't through any fault of my own but the availability of the players and that has cost us."
AFC Wimbledon finish the season 15th in League Two with 58 points from their 46 fixtures.