Bowyer had warned the players that the worst-case scenario would be the visitors taking the lead, and they did so after just seven minutes as Simon Church finished confidently from Dale Stephen's clever ball forward.
Rovers huffed and puffed for a way back into the game and although they had several half-chances, Jordan Rhodes denied by Ben Hamer in the first half and Jason Lowe seeing a volley deflect wide in the second, it wasn't to be for the home side.
"We spoke about them coming with a game plan and they were spot on with their game plan," the Rovers boss told Radio Rovers post-match.
"We felt that we were disappointed with their goal that we conceded because we felt it was hand ball from the lad.
"Had they not scored then we'd probably be looking at a goalless draw similar to the Huddersfield game.
"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.
"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."