Rovers are now unbeaten in three league matches after the victory at the Memorial Stadium with both goals coming in the final 20 minutes.
After a first half in which the hosts enjoyed the better of the chances, David Clarkson put the home side ahead after 70 minutes, following a number of missed opportunities.
Nine minutes later, John-Joe O'Toole pounced on a loose ball in the area, scoring his sixth goal in his last six home games to pull John Ward's side further clear of the relegation picture.
Victory would have seen Burton leapfrog Oxford United into third and move level on points with second-place Scunthorpe United.
In what was a goalless first half, Rovers had the best chance of opening the scoring, with Kaid Mohamed's cross headed against the bar by Clarkson.
Mohamed then went close with a low drive that went just wide before Adam McGurk's effort veered off target and there was just enough time for Lee Brown's free-kick to cause a goalmouth scramble before the half-time whistle blew.
Clarkson had an early opportunity after the break, only to slip at the vital time, before making amends with the opener 20 minutes from time.
The striker got on the end of Michael Smith's cross to register his first goal since December 21.
Clarkson was involved in the second as well - when his shot was parried by Rob Lainton, O'Toole was on hand to fire the loose ball home and kill off the game for the hosts.
The midfielder's 14th goal of the season proved to be the final effort of the match as Rovers moved eight points clear of the relegation zone.
Despite Burton's defeat, they will remain in sixth come the end of Saturday's games, although Southend United can go within a point of Gary Rowett's men with victory at York City.
