Bowditch handed Yeovil a dream start when he raced onto Gavin Tomlin's defence-splitting pass and beat Dons goalkeeper Willy Gueret at his near post after just 33 seconds.
Baldock levelled for Milton Keynes in the fourth minute when he sprinted onto Aaron Wilbraham's flick and expertly drilled in his seventh goal in as many games from an acute angle.
MacDonald restored the Glovers' lead in the 17th minute by slotting the ball underneath Gueret from 12 yards after another perfectly-weighted Tomlin pass.
Dons defender David McCracken escaped with just a yellow card for cynically tripping Bowditch as he raced through on goal before he headed Jason Puncheon's corner against the bar on the hour mark. But the Dons were not to be denied and Leven coolly converted his third spot-kick of the season to make it 2-2 in the 65th minute, after Wilbraham had been dragged down in the box by Terrell Forbes.