He will be re-evaluated this week.
"It was funny, we were talking about who on this defense is kind of the one that would hurt the most to lose and unanimously we talked about Boley," defensive captain Justin Tuck said. "He's that guy that gets everybody set up and lined up. I hope (the hamstring injury) is not as serious as it might have looked. We definitely need him."
Cornerback Aaron Ross also suffered a bruised quad injury that kept him on the sidelines in the second half.
Tom Coughlin did not have much of an update on the two injured defensive players after the game.
Boley was back in coverage and fell to the turf at the end of a play near the end zone. He got up and walked off the field under his own power but walked gingerly to the locker room. He returned to the sideline in the third quarter in warm-up pants and a T-shirt.
Boley, who also has been slowed by a nagging knee injury this season, entered the game with 42 tackles and one sack this season. He made three tackles in the first half against the 49ers before leaving with the injury.
Boley is a critical part of the Giants defense. He is the lone every-down linebacker for the Giants and has taken on a bigger leadership role this season while relaying the calls to the defense from defensive coordinator Perry Fewell.
Ohm Youngmisuk covers the Giants for ESPNNewYork.com. Information from The Associated Press was used in this report.