The 23-year-old notched his 13th goal of the season on the hour mark to end the Glovers' four-match unbeaten run, and hand Rovers just their second away league win of the season.
Bowyer reserved special praise for his £8 million striker - and insisted he has no problem with the Premier League interest being shown in him.
Bowyer said: "Jordan is a top lad, his manners are unbelievable, he's polite and popular at the training ground.
"His work rate is phenomenal, he never moans or gets carried away and all he's bothered about is his next goal - it's a fantastic attitude to have.
"He took his time with the goal, took a touch and picked his spot. I see it time and time again in training so it's no surprise.
"You saw today on that pitch there's more than one player who will attract Premier League interest, and I've got no problem with that as all of our players should want to play at the highest level. It's not just Jordan, we have a number of very good players.
"We thoroughly deserved the win. We played some really good stuff and I was delighted with the performance. To be an away team and come and put a performance in like that was fantastic.
"We controlled possession, especially in the first half, and we were just a little disappointed that we didn't convert more chances and make it more comfortable for ourselves."
Yeovil manager Gary Johnson urged his side to learn from their seventh home defeat of the season.
Johnson said: "It's a disappointing result but we mustn't be devastated about it.
"We didn't get our passing game going in the first half and kept giving the ball away, and if you do that against a top team in this division then you'll be in trouble.
"In the second half we kept the ball better, created a number of chances and hit the bar and the post. We were in the ascendancy, but then their goal came on the break against the run of play.
"We know they're a good side and we gave everything we had, but with a bit of luck and better judgment we may have got something out of it.
"I thought we controlled Rhodes well in the game, but he got into that position once and stuck the ball in the net.
"We have to learn from these games, but we're still learning about teams in the top half of this division who are looking to get into the Premier League."