San Jose jumped past Los Angeles into the fourth spot in the Western Conference playoff race while Calgary faded further from post-season contention with its fourth straight loss.
The only Calgary goal came from Mikael Backlund with 2:05 to go in the first period and that was the game's only score until the Sharks finally got to Miikka Kiprusoff in the third period.
Boyle tied it 2:40 into the final period with a slap shot and Pavelski delivered the game-winner with 2:06 to play.
Antti Niemi picked up the victory with 23 saves. Kiprusoff stopped 39-of-41 shots.