Scott Gomez also scored -- his first goal since February 5, 2011 -- and Carey Price made 31 saves for the Canadiens, who have won three straight games.
Matt Moulson and Mark Streit found the back of the net and Evgeni Nabokov made 28 saves in defeat for the Islanders, who failed to carry momentum from a 1-0 shootout win over the Philadelphia Flyers on Tuesday.
Montreal jumped on top just 1:23 into the game when Pacioretty corralled a loose puck in the neutral zone and moved to the right circle before snapping one past the blocker side of Nabokov on the first shot of the game.
The Canadiens extended their lead to 2-0 at 9:30 of the second period when Pacioretty gained the blue line and dished to David Desharnais on the left wing before getting the puck back and one-timing it past Nabokov from the high slot.
Montreal extended its lead to 3-0 with a power-play goal 9:50 into the third period when Raphael Diaz ripped a shot from the point that was kicked out by Nabokov, but the rebound came all the way out to Gomez, who fired it into the net from the right circle to end his goalless drought.
"Obviously I want to score," Gomez said. "But the team has to win."
New York finally got on the board with 2:41 remaining in the final stanza when Moulson batted a rebound home out of midair off a shot by John Tavares.
The Islanders then got within one with Nabokov pulled less than a minute later when Streit fired a slap shot past a screened Price, but Pacioretty completed his hat trick with an empty-netter with just one second to play to seal the win for Montreal.
"We had some chances on the power play," Islanders head coach Jack Capuano said. "We got pucks to the net late, but it was a little too late.'
Entering Thursday's action, New York had earned points in a season-high five straight games (3-0-2)...Montreal scored on its only power-play chance, while the Islanders finished 1-for-2 with the man advantage...The Islanders will host the Los Angeles Kings on Saturday, while the Canadiens will also battle the Toronto Maple Leafs on Saturday.