Rowett's side fell to second-half goals from Alfie Potter and Danny Rose after having defensive general Ian Sharps sent off by referee Michael Bull for kicking out at Dave Kitson, who escaped with a yellow card despite retaliating.
Rowett said: "I thought we were in control of the game, but that decision changed the whole complexion of the match.
"I've seen the incident again and if you're going to red card Ian Sharps for a kick, which didn't look particularly violent, then I thought it was in the rules of the game that if you raise both hands to push, it's also a red card.
"I'm not suggesting he (Kitson) was worthy of a red card, but you hear of it all the time.
"I just felt those decisions changed everything.
"Unfortunately, we conceded at a very bad time, early in the second half, and it was also a very poor goal to concede.
"We had more than enough bodies in there to deal with Potter and from thereon in it was a case of us trying to nick something.
"We had two or three half bits of opportunities in and around the box, but it was all over when they got the second goal."
Potter cashed in Burton's defensive indecision to waltz past three opponents and score with a deflected shot in the 50th minute.
Ssecond-placed Oxford sealed the three points five minutes from the end when Rose forced home Ryan Williams's cross from close range to sentence Burton to only their fourth home league defeat since the start of last season.