The Grecians took a first-half lead through Billy Jones but were never able to kill off the game. Nigel Clough's men always looked a threat and stunned a crowd of more than 4,000 with two goals in five second-half minutes from Darren Stride and Jon Shaw.
It only looked a matter of time before Exeter would take the lead. Tony Scully twisted and turned on the edge of the box and struck a shot just past the post.
Exeter took the lead in the 17th minute. Jones struck a free-kick from the edge of the box which was parried by the goalkeeper and the ball dropped just behind the line.
Jones rightly took the applause, but in truth the goalkeeper should have blocked the effort and it was a soft goal to concede.
Burton enjoyed their best spell of the game after falling behind. Shaw volleyed just wide from20 yards. Just before half-time Dan Bacon was found by Aaron Webster and the striker fired just wide.
After the break Burton continued to look dangerous. They never stopped working and got their reward with 11 minutes left on the clock.
Chris Hall drifted a deep cross from the right which was met by Stride, and the captain tapped home the rebound after his initial header was well saved by Paul Jones.
Worse was to come for the Grecians within five minutes. Keith Gilroy struck a powerful free-kick into the box and Shaw headed superbly past the goalkeeper from ten yards.
The goal stunned the Grecians but it was no more than Burton deserved and there could by few complaints about the final result.