In doing so, the Blackburn-born midfielder became only the third Rovers player to make their debut for the club at the age of 16.
Only two had managed that feat before Mahoney, Harry Dennison - the club's youngest ever debutant at 16 years and 155 days, and Ronnie Clayton at 16 years and 263 days.
At 16 years 337 days, Mahoney made his bow in the FA Cup defeat to Manchester City at the Etihad Stadium, with his manager more than pleased to see him out there.
"It is a fantastic place to come and make your debut against some great players," said Bowyer.
"We just thought why not and I was delighted with his performance.
"Since he's arrived he's done ever so well and I thought he was terrific when he came on.
"At 16 he didn't freeze, he had a great run and cross. He's got a lot of work to do but this should whet his appetite to do really really well. I'm delighted for him.
"That is the model that we want to develop, we want to develop good young players and he fits in that category."
Rovers are back in action this Saturday when they travel to the City Ground to take on Nottingham Forest.
Tickets are currently on sale priced £25.00 Adults, £18.00 Seniors (aged 65+), £12.00 Under 18, £6.00 Under 12. Call the ticket office on 0871 222 1444 to book.
Tickets will be available on the day of the game but prices rise by £2.