Playing for the second time in as many nights, the teams battled to a scoreless draw for almost 25 minutes before Joe Pavelski put a wrist shot past Miikka Kiprusoff. Torrey Mitchell added a power-play goal with 1:51 to play in the second and Nabokov did the rest.
Kiprusoff, who stopped 37 shots in Calgary's 3-2, series-opening win Wednesday, made 41 more saves Thursday. But he did not have the offensive support in Game 2, with the Sharks' defense closing down the Flames' attack.
Stephane Yelle, who scored twice for Calgary in the opener, was not credited with a shot on goal in the second game. The Flames also hurt their cause by sending a steady stream of players to the penalty box.
Calgary was called for seven minor penalties in the second period, virtually negating its hopes of keeping pace with San Jose.
The third game of the best-of-seven series will be played Sunday in Calgary.