Craig Conway's first goal for the club was enough to give them a 1-0 victory at the Madejski Stadium.
"It is a great win at a very difficult place to come," said the Rovers boss.
"They are a good team and they'll be in the shake-up for the play-offs, if not automatic, so it is a very good win for us.
"This is a difficult place to come, I think they've scored seven and five here recently so we knew the challenge ahead.
"The lads took that challenge on and we scored a great goal on the counter and their goalie has had to make a couple of good saves as well. We didn't rest on our laurels once we took the lead.
"So we are pleased with how we went about it and kicked on in that second half to keep the clean sheet."
Rovers looked to be seeing the game out comfortably, but there were added nerves when an additional nine minutes were shown at the end of the ninety.
"You can imagine what I thought when the board goes up and you see nine, but we dealt with the added time," added Bowyer.
"We were throwing our bodies in front of the ball, we defended the goal magnificently well.
"You knew they were going to come back and have a go at us, but we worked very hard and I am pleased with how we went about it again."