Manager Paul Sturrock felt Southend were not good enough against Burton and ultimately deserved to lose at the Pirelli Stadium.
Substitute Blair Sturrock headed Southend back into the game at 2-1 early in the second half but the Essex side could not push on.
"I felt sorry for the travelling fans because you have to go our and earn the right to play and at times we didn't do that," said Sturrock. "Second half we went out on the front and dictated from the start and it might have been different if we had got back to level terms. But as the game unfolded you could see the match fitness and sharpness seep away.
"If we had gone in at half-time and then got the equaliser it would have been a completely different ball game but, to be fair, by the end of the game we didn't deserve to get anything out of it.
"Burton's third goal was a great finish into the top corner and you could see a few of our heads went down after that."
Sturrock added: "The important thing is we have got a match under our belts after a longer lay-off than most teams. We've got another game on Tuesday (at Cheltenham) but it will still be a case of chucking the dices up to see who is going to be able to play."