It had started well for Rovers after Jordan Rhodes had opened the scoring for the home side, but two goals in six second half minutes saw the visitors claim all three points.
"I thought the result was a bit harsh on us," Bowyer told Radio Rovers. "We are bitterly disappointed, there is a lot of hurt in there.
"The start of the second half Jordan Rhodes goes through and it hits the post, if it goes in then it is game over. You are talking fine margins, we could have been two goals up.
"That said we are disappointed with the manner of their two goals. They were very direct, they kept pumping balls into our box and we are disappointed with how we defended those two. We have to mark better from the set-play.
"You have to look at how strongly we finished at the end, Rudy has had a couple of chances, Lowey as well, and Liam Feeney has put a couple of good balls in.
"We kept going, we kept showing the fight, but we are disappointed.
"If we'd have won today, and we got ourselves into a good position to do, we'd have been three points off the play-offs."
Rovers are back in action this Wednesday night when AFC Bournemouth are the visitors to Ewood. Ticket are on open sale priced £15 Adults, £10 Seniors and £5 Juniors. Book online today at www.onerovers.co.uk
and collect on the day of the game.