Rovers took the lead through a Jordan Rhodes penalty but strikes from Jermaine Johnson and a Leroy Lita spot kick saw Sheffield Wednesday lead at the break.
The second half saw Bowyer's side camped in the Wednesday half, eventually getting their reward when Scott Dann headed home with just under 20 minutes to go.
Such was the dominance it looked like it would be Rovers who would go on and claim all three points but a 25yd wonder strike from Johnson settled the match in the home side's favour.
"I thought it was important that we started off on the front foot and we did," said Bowyer after the game.
"The penalty settled us down and I thought we rightly took the lead.
"Then we weren't competitive enough with their first one and then I think the referee has evened it up a little bit with theirs as we think it is a bit soft but it is avoidable.
"At half time we got in and said that we had to keep trying and keep playing and that is what we did.
"I thought we totally dominated the game second half. We were camped in their half so not to come away with anything is a blow.
"I think you can take a lot of positives out of the game with the way we played, the way we closed down and when it went 2-2 I felt there was only going to be one side that would go on and win it and that was us.
"We were done by a wonder goal, you've got to give credit to the lad.
"We can take positives from how the lads have gone their business today, especially with the way we performed in the second half.
"We leave here disappointed because we haven't picked up the points we deserved because of how we played."