Neil Woods’s side were a goal down at the break and, despite an improved second-half display, conceded a second towards the end of the game.
Burton were on top in the early exchanges, but were restricted and didn’t create any clear-cut chances in the opening stages at St. George’s Park.
But Town struggled to clear the ball on 15 minutes and the home side finally got their breakthrough as they scored with a strike from the edge of the area.
But the young Mariners responded well and hit the bar twice in quick succession through long-distance efforts from Evan Khouri and Luis Adlard.
And in-form forward Lennon Stead also went close to equalising for Town, after some neat individual work.
Town continued to threaten in the second half, and again went close with long-range efforts – this time from Owen Davey and Joe Starbuck.
But the Brewers doubled their lead as they tapped home from a corner to make it 2-0.
The remainder of the game became a possession battle with no team creating any further chances.
Town welcome Chesterfield to Cheapside in the Youth Alliance Cup Group on Saturday (11am).