A brace from Paddy Madden inflicted 10-man Dons - who defeated Barclays Premier League side QPR on Saturday - to their first defeat in 2013, with the visitors having goalscorer Antony Kay dismissed in the second half.
After referee Mick Russell passed a late pitch inspection in Somerset, it was the hosts who dominated the opening exchanges.
On-loan midfielder Matthew Dolan's low drive was saved before Madden fired wide.
The Glovers, who were playing their first game since January 12, took a deserved lead on 25 minutes when Kevin Dawson found Irish compatriot Madden, who swept home to notch his 12th goal of the season.
The visitors struck back 10 minutes later when Kay rose unmarked to head Shaun Williams' corner past Marek Stech.
Kay was shown a straight red card shortly after the hour mark for an off-the-ball clash with Madden - sparking an ugly confrontation between both sets of players.
However, Madden had the last laugh in the 78th minute by grabbing his sixth goal in three games to keep his side within touching distance of the top six.