Rovers went behind to Simon Church's seventh-minute goal but were unable to find a way back into the game.
While Bowyer was happy with his players' response to going a goal behind, he feels that luck was not on their side.
"I thought we responded quite well but we were just lacking that quality and creativity in the final third. You certainly couldn't fault the players for their work-rate or their efforts," he told Radio Rovers.
"The ball just didn't bounce a couple of times for us, it just didn't quite run for us. It was one of those days for us today."
The result leaves Rovers seven points off the playoff places.