Cole Caufield had an assist, and Sam Montembeault made 30 saves for Montreal (18-37-11), which was playing the first of a four-game road trip.
"I wouldn't say I'm disappointed with the loss because I felt like we got better as the game went on," Canadiens coach Martin St. Louis said. "It's our third game in four nights and we tied it up late, so I'm happy with the way the guys fought and crawled back and almost won it."
Mike Hoffman thought he had won the game on a breakaway for Montreal with 54 seconds remaining in overtime, but it was ruled no goal following a video review that showed the puck hit the right and left post before deflecting out.
Rem Pitlick tied it at 2-2 with 42 seconds left in the third period during a 6-on-5. He scored on a quick shot near the right post off a no-look backhand pass from Christian Dvorak.
"It's a tough one to lose, but we fought hard," Montembeault said. "We didn't have much for most of the third period, but the guys stuck to the plan and we end up scoring on that 6-on-5. I was really happy with the effort of the guys."
Hughes made it 1-0 at 19:16 of the first period after stealing a pass attempt by Montembeault in the right circle and scoring on a wrist shot.
"I saw the puck in front of the net and all the guys were changing on my short side, so I didn't want to shoot it at the bench to get a too many men penalty," Montembeault said. "I tried to go on my backhand, and I was not even close. I gave it to Hughes and he scored. That was my bad. I should have just made a better pass on my backhand or thrown it to the glass."
Hughes extended New Jersey's lead to 2-0 at 14:16 of the second period with a wrist shot from the right circle on the power play.
"On a personal note, I feel good on the ice," Hughes said. "I got a good little thing going here."