The former Watford man has been with the Pirates since New Year's Eve and he has become an instant hit at the Memorial Stadium.
Rovers have extended the deal for the maximum period allowed for an emergency loan. This means the midfielder will be with the npower League Two strugglers for all but the last four games of the 2012/13 season.
"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," manager John Ward told the club's official website.
"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."
- Sports & Recreation