Patrick Marleau and Mike Grier also scored for the Sharks, who avenged a decisive 4-1 loss to Minnesota last month with two early goals followed by two periods of strong defence. Nabokov was outstanding in just his second win in five starts, snapping the Wild's four-game winning streak at the Shark Tank.
Todd White scored and Manny Fernandez stopped 27 shots for Minnesota in the opener of a five-game road trip after playing just four games away from St. Paul all season. The Wild have lost three of four after a 9-1 start, including their first back-to-back defeats of the season.
Sharks coach Ron Wilson, dissatisfied with his high-scoring club's 5-on-5 play, broke up his top line around Thornton, putting Mark Bell on Marleau's line and dispatching Jonathan Cheechoo - the NHL's top goal-scorer last season - to the third line. The move didn't end Cheechoo's goal drought, which reached seven games.
After Grier's early goal, Thornton got just his third goal in 16 games this season - and his first in eight home games - when he redirected rookie Matt Carle's shot past Fernandez midway through the first period. White answered for the Wild when he was left alone in front of Nabokov.
After 41 scoreless minutes, Marleau gave Nabokov some cushion with a goal on an odd-man rush with Mark Smith with 4:55 to play.
Despite the loss, the Wild's five-game road trip is something special: More than two-thirds of the club's players and executives are traveling through California with their fathers, who sat in the stands together wearing Minnesota's alternate red jerseys with their names on the back. With three days off in Los Angeles before their next game, they planned to hit the Universal Studios theme park Wednesday.
San Jose begins a four-game road trip in Los Angeles on Thursday.
Notes: Cheechoo left the ice less than five minutes into the game after getting hit in the face by a shot, but returned for the second period wearing a visor. ... Sharks enforcer Scott Parker made his first appearance of the season, returning from injured reserve to play a handful of shifts. Ville Nieminen and Curtis Brown were scratched. ... Minnesota's Wes Walz was scratched with a leg injury for the third time in four games. He scored his 100th NHL goal in the Wild's previous trip to San Jose.