In a repeat of last year's corresponding fixture, Rhodes settled matters with his ninth goal in the past seven games, while also ending the Hornets' three-match winning streak in the process.
The win put Rovers eighth in the league after 10 games, four points below sixth-place Blackpool.
"I don't get bored of talking about Jordan Rhodes. He's a fantastic lad who works tremendously hard," Bowyer said.
"He's a great finisher, knows where the goal is and deserves the plaudits because of his ability and finishing.
"When you've got the firepower we've got in terms of Jordan, Bestie (Leon Best) and (Josh) King and we've got DJ (Campbell) still to come and Ruben Rochina, if we can stay in games and keep clean sheets - we've got the belief that we can go and win games."
Bowyer also spoke in glowing terms about defensive duo Scott Dann and Grant Hanley who have started every league game together this season and were responsible for a second consecutive clean sheet at home.
"They've been magnificent and it gives you the platform to build from," he said.
"You saw first half how Watford got into their groove with their passing game but we defended very well, were organised and disciplined and grew into the game and took a confidence from keeping a clean sheet in the first half."