Barnsley were no match for a hard-working Rovers side who lead at the break thanks to first half strikes from Joshua King and Ruben Rochina.
The home side were given hope when Stephen Dawson pulled one back with 14 minutes to go but Rovers' nerves were eased when Jordan Rhodes fired home deep into injury time.
"It is brilliant for the lads to get the three points," said Bowyer after the game. "I can't praise them enough.
"They were magnificent yesterday in training and they've done the same again this afternoon.
"The level of the performance from everybody was first class. From the way we defended, through to the pace that we showed in the goals that we scored. I'm truly proud of the way we have gone about it.
"We have got some good players at the club and they have gone about it the right way today, they really worked hard, I know it is a cliche but I can't praise them enough.
"The players spoke yesterday of how they wanted to do it for the club and for the fans, they've ended the year on a high by coming here and winning three points, now they have to try and reproduce that on New Years Day."