The victory hands the Brewers fourth spot in the table and home advantage in the play-offs as they now prepare to face Bradford over two legs.
Gills boss Martin Allen included three teenage debutants in his line-up and a more experienced Burton side came from behind to preserve the best home record in the division.
Myles Weston struck from the penalty spot for the Gills in the ninth minute after Bradley Dack had been tripped by full-back Aaron Webster.
Burton were back on level terms in the 33rd minute when Billy Kee rattled home the rebound after a thunderous shot from Jimmy Phillips had hit a post.
Phillips was again the provider six minutes later with a low cross that was tapped home by Michael Symes to give Burton the lead.
Adam Birchall was denied a Gillingham equaliser straight after the break by Stuart Tomlinson's brilliant reflex save.
And the Gills were unable to contain Phillips as the winger produced the perfect cross for substitute Calvin Zola to head Burton into a 3-1 lead in the 63rd minute.
Gillingham sub Nathan Nyafli had an immediate impact when he stole on to the end of Sam Muggleton's long throw-in to reduce the deficit three minutes later, but Burton ran out winners.