O'Toole joined the Pirates on New Year's Eve and has already made a huge contribution towards the club's battle against relegation, making four starts and scoring one goal.
He will now remain at the Memorial Stadium until April 2 - taking his loan up to the maximum 93-day period.
Rovers boss John Ward worked with O'Toole during his three-year spell at Colchester as assistant boss and then manager, which was eventually brought to an end in late September.
Ward told Bristol Rovers' official website: "It is great news that John-Joe is here to stay, it is what everyone at the club wanted and the other players are all very happy.
"There is a 24-hour recall clause, but that was something that Colchester United wanted, and I fully understand that.
"He brings a strength and a character to the club and he wears his heart on his sleeve. He is a ball winner and always gives everything.
"He is what we need at this club, he cares about the team and that is why he has endeared himself to the fans."
