Second-half goals from Adam Rooney - who spent a month on loan with the Glovers in 2007 - and substitute James Collins ended the hosts' nine-game unbeaten home league run.
MacDonald reserved praise for defender Nathan Thompson's sparkling man of the match display.
He said: "I'm delighted for the players and the supporters who travelled down here because they were tremendous and got behind the lads.
"You can see the passion between the players and the fans which is great. Personally, I think we can play better and have played better and lost in the last four games, but sometimes to win ugly is important for the team as well.
"They probably had more possession in the first half but we had more clear-cut chances. We just got a little bit untidy and nervy in the second half, but when we scored the first we kept the ball much better and I always thought we had the chance to get a second.
"Nathan was fantastic and he deserved the man of the match award. I just wish he wouldn't get booked as many times.
"I'm working on the premise that we won't be out of a transfer embargo, but you saw how the players played and how they have played all season. You don't get into this position without being a decent side.
"I think Yeovil had won the most home games out of anybody so far, and although I wouldn't say we were comfortable, I think we deserved to win the game.
"It's going to be up and down for the next eight games."