Rovers' record signing didn't know too much about the 84th minute leveller as Burnley defender Michael Duff's intended clearance rebounded off the striker and into the back of the net for his fifth goal in three games.
But Bowyer felt it was just reward for the hard work put in by the 23-year-old.
"He chased everything and we are fortunate that he was in the right place at the right time and you can't buy that," said the Rovers boss.
"He's played up there on his own today, worked ever so hard and he's scored a goal again.
"So we are delighted for him, the game is about opinions and our opinion on Jordan Rhodes is what a fantastic striker he is.
"There's no chance you can take that goal off him, the last touch is off Jordan, and I'm not fighting him even with one hand."
Rhodes and Rovers are back in action this Tuesday night when they travel to face Leicester City.
Supporters who are planning to watch the game should allow extra travelling time.
Roadworks in Leicester city centre and in particular near the King Power Stadium has lead to heavy matchday delays so Rovers fans should set off in plenty of time to make the 7.45pm kick-off.
Tickets are still on sale for Tuesday's match with advance purchase tickets going off sale at Ewood on Monday.
Advance purchase prices are £28.00 Adults, £25.00 Senior Citizens aged over 65, £25.00 Under 22s, £18.00 Under 18s, £9.00 Under 12s and £7.00 Under 8s.
Tickets will be on sale on the day of the game from the King Power Stadium but supporters should note that prices will rise by £2 on matchday.