Boston had blown a two-goal lead in the third, but Seguin scored on the second chance of the shootout when he blew a wrister past Carey Price.
Tim Thomas then stopped Lars Eller's wrister with his blocker to give the Bruins their third win in the past five games.
"I've been lucky so far in shootouts but I'll take it," said Thomas. "It was a bit more passionate game that we played tonight. We brought the effort with team energy and part of that was how Montreal came at us."
"I'm sorry to say, when we don't come out with two points at this time of the year, it's so frustrating," said Pacioretty. "We know we could have gotten two points because of the way we played in the third. We can't let games like that go because of our situation."
Boston held a 3-1 lead going into the third, but the Canadiens made it a one- goal game just 3:34 in when Pacioretty's one-timer from the slot trickled behind Thomas.
Zdeno Chara's miscue led directly to Montreal tying the game. The big defenseman held the puck near his left circle and used a lazy pass to try and get it over to the right, but Cole was there for the easy pickoff and he switched to the backhand before putting it past Thomas with 8:48 to play in the third.
The Bruins scored late in the first period to take a 1-0 lead. A blind backhand clear by a Montreal player behind his own net was picked up by Ference, who flung a wrister on net from the right circle that beat Price to the shortside with 2:51 remaining.
Montreal tied the game while shorthanded 99 seconds into the second as P.K. Subban skated down the right wing and from down low centered the disc for a redirect by Darche.
The Bruins, though, took the lead back at the 5:07 mark of the second as Pouliot skated in with a defender in front, and made a sharp move to get around him and snapped a wrist shot in from the slot.
Skating on the man advantage, Boston took a two-goal lead when Seguin sent a pass from the left point to the side of the net where Bergeron was able to put the puck in off the right post with 5:27 left.
Boston continues its six-game road trip in Winnipeg on Friday...Montreal plays in Buffalo on Friday...Boston went 1-for-6 on the power play while Montreal was 0-for-4.