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 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."
Despite making five changes from the side that defeated Wigan last time out, Watford boss Gianfranco Zola was critical of the number of games his side has had to play in the past three weeks.
"I am disappointed with the performance and the result," he said.
"I knew it wouldn't be a great game of football today because it is the sixth game in 17 days so I wasn't expecting great quality.
"But the way the game was going, I was not expecting to concede that goal either because we had defended well from set pieces before that. It is just one of those where we lost attention and it cost us greatly today."
The Hornets went into the game as the league's highest scorers and Zola could not hide his disappointment that his side seldom looked like adding to their tally.
He said: "We were certainly not brilliant [going forward]. It wasn't only the penetration that was poor; it was also the quality of the passing in midfield was not as good as normal.
"I think a lot is a consequence of there being too many games and you can't always play with the same quality."
He added: "It is not only us; all I am saying is the quality cannot be great."