The Sky Bet Championship clash was all but beyond Blues with less than an hour played as the Posh hit three goals without reply.
However, Blues certainly showed character to not concede further goals after Gary Gardner’s red card and even kept creating chances until the final whistle.
Speaking post-match, the Head Coach gave an honest assessment of events at the Weston Homes Stadium.
He told reporters: "It's not acceptable. We can't come away from our strengths and today we did. I think that the Wednesday to Saturday turnaround is hard, they [Peterborough] had the extra days rest and to me, it showed, they were first to every second ball, they were sharper.
"Everything we are good at we just couldn't physically do. It wasn't just one or two players, there was a lot of them, near on all of them. There's a reason and it is three games in one week, it's too much.
“We have got to recharge our batteries and we have a full week now. Then we can try and put things right again.”
Bowyer was able to take postives from an improved showing after the break, with a number of opportunities falling his side's way.
But he was aware that his men cannot be too aggrieved at the outcome and said: "Second-half I thought we came out and caused them problems. But just all day nothing fell for us.
"At half-time, we changed things around and started the better side. Our player made a pass and it hits one of our own players on the heel and then they go and score. If we score that next goal then we are in the game.
“You can't make excuses they were the better team."
The Gaffer also had no complaints about the challenge from Gardner which saw his team reduced to ten men in the 65th minute.
He explained: "It was an honest attempt to win the ball. I can understand why he went for it and he just overran it. I have seen people sent off for the same thing, so I can understand why it was a red card but there was no malice in it."
Nearly 4,000 fans made the trip east to back the team and remained vocally behind the players throughout, with Bowyer hugely grateful for their support.
Praising the travelling Bluenoses, the boss said: "I know what they bring from start to finish and I have to credit them. I have to thank them for non-stop singing and staying until the end. We are 3-0 down, they blow the whistle and they are still singing. That is some doing and passion for your football club. I'll apologise for today's performance."
You can hear more of Bowyer’s post-match thoughts below, as he spoke with BluesTV.