Pacioretty ran his season total to 22 goals, recording the only tallies of both the first and second periods.
Scott Gomez then scored his first goal of the season in 24 games for the Canadiens, but New York rallied to within one on goals from Matt Moulson and Mart Streit in a span of 48 seconds late in the third period.
Pacioretty concluded his hat trick with an empty-net goal a second before the final horn sounded.
The goal for Gomez was his first in just over a year. He has 168 goals in 889 career games spread out over 12 NHL seasons.
Montreal won its third in a row, getting 31 saves from Carey Price. Evgeni Nabokov stopped 28 shots for the Islanders.