Devin Setoguchi scored his team-high 14th goal for the NHL-leading Sharks, who opened a gaping 13-point advantage atop the Pacific Division standings over the second-place Ducks with Nabokov's 41st career shutout. It was punctuated by a brilliant kick save on Corey Perry in the final minute.
Jonas Hiller stopped 25 shots for the Ducks, who lost for the third time in nine games. The longtime rivals' third meeting of the season ended with a handful of scuffles and major penalties.
The Sharks survived with Nabokov, who has played seven straight games for the Sharks since returning from a three-week injury absence. The Vezina Trophy finalist hasn't lost in regulation since Oct. 24 at Florida.
After an overtime loss to Edmonton last Saturday that snapped the Sharks' nine-game winning streak, they had four days off before this showdown. San Jose used the rest to beat the Ducks at their own physical game, winning for the 17th time in 20 games with puck possession and disciplined hockey -- and a few well-placed shoves.
The clubs' long-simmering dislike erupted with 5 minutes left when Milan Michalek knocked Perry to the ice in response to an attempted open-ice check. Chris Pronger, Chris Kunitz and San Jose's Joe Pavelski all got involved, but only Michalek and Perry got penalties.
Another big shoving match erupted with 20.4 seconds left with many of the same combatants along with Sharks defenseman Rob Blake, who got sent off with a spearing penalty. Michalek and Anaheim's Scott Niedermayer also got misconduct penalties during the fracas.
The Ducks were responsible for the biggest of the Sharks' five losses this season, shutting out San Jose 4-0 on Oct. 17 to end the club's unbeaten start. The Sharks also beat Anaheim 4-1 in the season opener.
The rivals don't meet again until March 15, when they'll play the final three games of their season series in three weeks.
The NHL's highest-scoring team added two goals to its total of 104, but both were good-looking scores by the Sharks' two leading goal-scorers. Marleau got the Sharks' first on a long shot late in the first period.
Marleau already has 13 goals while playing with Joe Thornton and Setoguchi on the Sharks' top line. He had 19 last season while struggling with confidence and chemistry until the trade deadline, when the Sharks' franchise scoring leader's game returned.
Anaheim managed only intermittent offensive pressure despite a shot advantage, and Setoguchi increased San Jose's lead when he whipped home a rebound of Marleau's shot midway through the second.
Notes:@ The Sharks again played without RW Jonathan Cheechoo and D Brad Lukowich. Cheechoo is close to returning from his upper-body injury after practicing during the Sharks' four-day layoff, while Lukowich still is hobbled by a groin injury. ... After beating St. Louis 4-2 on Wednesday, the Ducks waited until Thursday morning to fly to San Jose. ... San Francisco 49ers left tackle Joe Staley led a contingent of several teammates at the game.