Quigg, the former WBA super-bantamweight champion, was looking to prove he remained at the elite level but the Bury fighter struggled with the superior movement and work-rate of his Irish opponent.
While Quigg never looked to be seriously hurt, he was wobbled on a couple of occasions and there was a sense he could have been pulled out before trainer Joe Gallagher eventually threw in the towel in the penultimate round.
The 31-year-old offered no excuses after being stopped for the first time in his 40-fight professional career before admitting he will in all likelihood bow out from the sport.
"He was the better man on the night," Quigg told Sky Sports. "After the fourth round, it didn't feel like it was there, I was just chasing it. But no excuses, the better man won and fair play to him.
"I'm a realist, I don't kid anyone. I believe at my peak, I would have won this, no problem, and that's taking nothing away from Jono. In my day I believe he wouldn't have lived with me.
"On this performance and how I felt, I don't know if there's much left, to be honest."
Quigg (35-3-2, 26KOs) defended his version of the 122lb world title on six occasions, four times at Manchester, where he lost to Carl Frampton in a unification bout four years ago.
After linking up with highly-respected trainer Freddie Roach, Quigg stepped up to featherweight and challenged Oscar Valdez in March 2018 but missed weight which meant the Mexican's WBO title was not on the line.
In a brutal 12 rounds in which both fighters sustained injuries that would sideline them for several months, Quigg dropped a unanimous decision.
A low-key win over the unheralded Mario Briones followed later in the year and that was his last outing until his date with Carroll (now 18-1-1, 4KOs), having returned to trainer Gallagher.
Quigg added: "I couldn't have achieved any more because I gave it everything; I cut no corners, I gave it 150 per cent. I've been world champion, I've had a great career.
"I've been here, sold out arenas. There's no place I would rather have boxed and if this is it then thank you to everyone who has come out to support me throughout my career."
On the undercard, British heavyweight Hughie Fury (24-3, 14KOs) returned to winning ways with a third-round stoppage of the little-known Pavel Sour.
