The 22-year-old, who has played in a variety of positions for Rovers during his burgeoning career, filled in at centre-half after Grant Hanley had been red carded, with Bowyer delighted with the way he performed.
"I thought Lowey was magnificent, absolutely magnificent," said Bowyer after the game.
"Credit to the lads, initially, they put Tommy Spurr there, they did that themselves, but we just felt that two left-footers in the centre half position might have been a little dangerous for us.
"So we put Lowey in there and kept Tommy in his natural position and it was only one change then so to speak.
"I thought he was brilliant, I really did. I feel sorry for him and the rest of them for how much they put into it.
"He just slotted in there and some of his decisions and bravery was magnificent. It is full credit to him."
Rovers and Jason Lowe are back in action after the international break with Charlton Athletic the visitors to Ewood Park on Saturday 18th October.
Tickets are on open sale priced from £15 for Adults, £10 for Seniors and £5 for Juniors. Book online today at www.onerovers.co.uk