The team's Twitter account said Gabbert "was coming out of the game anyway."
Gabbert connected on 13 of 16 passes for 165 yards and a touchdown before leaving the game in the second quarter. His touchdown came on a 5-yard pass to tight end Allen Reisner.
"Gabbert, 23, threw an incomplete pass on a third down that would have been his last play of the game regardless, but his hand collided with the helmet of a Jets player on the follow through of his pass," Adam Stites of Big Cat Country reports.
Chad Henne took the reins from Gabbert at that point.
It's not yet clear how the injury will affect Gabbert or the Jaguars' plans at quarterback. The Jaguards' Twitter account says more information will be available after the game.
Gabbert completed 58.3 percent of his passes at the helm of the Jags in 2012, good for 1,662 yards. He threw nine touchdowns and was intercepted six times.