Some 2300 Rovers fans were in attendance at Bloomfield Road to see a brace from Rudy Gestede earn the visitors all three points.
Bowyer was full of praise for the backing his side received, more than playing their part as Rovers claimed their first victory of the season.
"They were outstanding," said the Rovers boss post-match.
"In particular the fact that in the last ten minutes we needed them and they never shut up. They were brilliant at the end.
"It helps, it really does help, and it is a good day out when you can send your fans home happy."