League Two champions Gillingham suffered their third away defeat of the season as Burton sealed fourth place.
Myles Weston converted a penalty for the Gills before Billy Kee rattled home an equaliser after a thunderous shot from Jimmy Phillips had hit the post.
Burton's Michael Symes tapped home a low cross before Calvin Zola headed them into a 3-1 lead.
Nathan Nyafli was on the end of Sam Muggleton's long throw-in to reduce the deficit, but Burton ran out winners.
VIEW FROM THE DRESSING ROOM
Gillingham manager Martin Allen and chairman Paul Scally told BBC Radio Kent:
"Supporters are going to be happy when they see a performance like that. That's the subs from Wimbledon plus six youth players making their debuts.
"If you can't be inspired by that as a supporter, you've got a screw loose.
"There's a good connection here between the fans and the players, it's been a good 11 months and this is my challenge with the backing of the boss to go again."