After defeating Reading 1-0 at the Madejski seven days ago the Rovers boss called for his side to match that against Bolton Wanderers but it was the home side who were the better throughout.
After chances came and went for both sides, Medo Kamara opened the scoring for the Trotters at the midway point of the first half, but key goals either side of the break from Joe Mason and Jay Spearing put the game beyond Rovers, before substitute Andre Moritz added a fourth in injury time.
"We've conceded four poor goals by the standards that we've set ourselves," said the Rovers boss. "There are no excuses for that.
"I think the first goal was crucial. Before that Bogdan has made two outstanding saves, one from Jordan and one from Markus.
"We can't perform like we did against Reading and then a week later come here in a local derby and perform like that.
"We demanded passion off them and I don't think we got enough off the players on that.
"Obviously the centre-half position didn't help us but there are no excuses like I say. When you pull the jersey on for Rovers we expect more than what we got off them today."
Rovers trailed by two at the break with the manager shuffling his pack, introducing Luke Varney and Corry Evans at the start of the second half, but Jay Spearing's effort two minutes later killed off any chance of a comeback.
Bowyer added: "We went for it, we had to, we put three up front and had a go.
"But we then suffered the sucker-punch of conceding straight after half-time, it was disappointing.
"We just have to regroup now, we'll debrief this game, look at the good points and more importantly look at the bad points because there were more bad points than good points today for us."
Football returns to Ewood with two games in four days as Rovers take on Burnley on Sunday and then AFC Bournemouth the following Wednesday.