The 31-year-old raced clear to slot the ball home 15 minutes from the end and maintain the Dons' 100% home record.
The Dons controlled a low-key first half and Luke Chadwick had a curling shot superbly tipped wide by goalkeeper Marek Stech from Daniel Powell's cutback as Yeovil defended resiliently before the break to frustrate the hosts.
Yeovil upped their game after the interval and Dominic Blizzard had a fierce drive pushed over the crossbar by David Martin before Luke Ayling's header was cleared off the goal-line by Darren Potter.
But the Dons regained control and Dean Bowditch fired into the side-netting before MacDonald netted the winner after 75 minutes, racing clear on to Darren Potter's chip to slot the ball past Stech.
Potter also had a low drilled shot saved well by Stech late on, while MacDonald had a goal ruled out for offside as the Glovers' 100% record on the road came to an end.