Gary MacKenzie gave the visitors a 64th-minute lead, but Jordan Rhodes rescued a vital point for Rovers, who parted company with boss Michael Appleton last week, with 11 minutes remaining.
"There's a lot of respect there for Michael Appleton and it was a decision that shocked the players," said Bowyer.
"To their credit they got on with their work and had a right good go.
"I thought we started nervously which was to be expected a little bit with what's gone off at the football club, but once they settled down they showed a good composure to make some passes.
"It's a bit of a sucker punch when they go and score - I've seen it on the video and it's a foul on Jason Lowe, so we're a bit disappointed about that.
"Full credit to the players, the way they responded was magnificent. They could have felt sorry for themselves but they didn't.
"We're fortunate to have Jordan, who's scored as many goals as he has this season.
"I thought we had a nailed-on penalty - I can't see how he (referee Mick Russell) has not given it, he's only five yards away."