Patrick Marleau, Dan Boyle and Ryane Clowe scored for the Sharks, who moved to 17-0-2 at home this season and 25-0-3 in their last 28 as the host dating back to last year. Their run of points in 28 straight home games is nine shy of the NHL record of 37 games that was set by the Montreal Canadiens in 1976-77 and 1977-78 (31-0 with 6 ties).
It was just their fifth win ever over the Rangers, beating them for the first time since October 22, 2001.
San Jose, coming off a 6-0 loss at Detroit, avoided dropping its third in a row for the first time this season. The Sharks lead the NHL with 55 points and are 26-4-3 on the season.
Thursday's loss to the Red Wings snapped San Jose's 15-game point streak (12-0-3), but two nights later they rode Nabokov's impressive showing as he stopped all 17 shots that came his way in the third period.
Nikolai Zherdev and Ryan Callahan had the goals for the Rangers, while Henrik Lundqvist made 27 saves. New York had its three-game win streak broken.
Callahan's goal midway through the second on a rebound brought the Rangers within 3-2, and even though they constantly pressured the San Jose zone in the third period, Nabokov was equal to the task.
That included the Sharks killing off a Joe Pavelski hooking penalty for two minutes to start the third.
Boyle scored during a two-man advantage 4:27 into the game on a one-timer from the left circle. Clowe scored 25 seconds later from the right side of the net.
Zherdev netted one shorthanded at the 10:34 mark of the first on a blast from the left circle, but Marleau scored 6:20 into the second on a shot from below the right circle.