Rudy Gestede set them on their way with his seventh of the season, a stunning strike on nine minutes, before Tommy Spurr fired home early in the second half to give the home side a comfortable victory.
"I think for an overall 90 minutes it was our best display of the season," Bowyer told Radio Rovers.
"We've had good 45 minutes and good patches of play, but for a full 90 minutes I think so.
"We started the game magnificently well and we continued that all the way through. We could have had more goals, but after a clean sheet and two good goals again, we're delighted."
Rovers opened the scoring in sensational fashion on nine minutes when Rudy Gestede unleashed a thunderbolt of a shot from distance that beat Robert Green all ends up.
The young Frenchman had hinted that he had that in his locker after firing over the bar from a similar position at the weekend, but on this occasion he made no mistake.
"He nearly scored on Saturday so we knew he was capable of doing that," added the manager. "Saturday was very close but obviously today was even better for us."
After a strong first half Rovers then grabbed a deserved second as Tommy Spurr bagged his third of the campaign with a low shot that beat Robert Green.
'We needed it, we knew we would need it, and when we got it it settled everybody down," admitted Bowyer.
"It was a well-worked goal, we got a bit of luck with it squeezing through but our build-up play was excellent.
"The players were outstanding, all of them."