Rovers dominated the first half but it wasn't until the 47th minute when they took the lead, Jordan Rhodes crossing for Rudy Gestede to head home.
But the visitors came back into the game and in the closing stages drew level, Patrick Bamford finishing well six minutes from time.
Speaking to Radio Rovers, the manager said: "I think when you go 1-0 ahead you hope you can see it through, but you have to remember the level of opposition we are playing. They've been on a fantastic run.
"It was a great goal from Rudy, I thought the two of them linked up very well today. I'm delighted with they are starting to shape up them two.
"We knew what we were doing when we brought the big man in and I thought he was outstanding.
"We rode our luck a little bit in the second half with one or two opportunities, but when they do equalise it is a fantastic strike from the kid. You have to take your hat off."
Rovers were once again left to talk about penalty decisions not give. Todd Kane appearing to be fouled in the box by Craig Forsyth but the referee was unmoved.
Kane, to his credit, tried to play on, eventually shooting wide.
"We tried to get back again and had a claim for a penalty for sure," added Bowyer. "A lot of our players stay on their feet perhaps too much. But Todd shouldn't have to go down for it to be a penalty.
"You saw the impact of giving a decision that wasn't one last week and there you go again.
"The players are a little bit disappointed but we've just said to them it is about picking up points so lets see where we are after we've played Barnsley and Blackpool.
"If we can't get three then we have to make sure that we got one and that is what we've done today.