Marc-Edouard Vlasic, Patrick Marleau and Brent Burns, into an empty net, also scored for the Sharks (4-0-0).
San Jose beat the Canucks 4-1 in both teams' season opener after sweeping Vancouver four straight in the first round of last year's playoffs. Joe Thornton and Logan Couture added two assists.
San Jose, which also won all three meetings during the 2013 regular season, has not lost to the Canucks since Jan. 21, 2012.
Sharks forward Tomas Hertl, who became the talk of the NHL after scoring four times in Tuesday's 9-2 win over the New York Rangers, was held pointless.
Mike Santorelli scored for the Canucks (3-2-0), who got 25 saves from Roberto Luongo.
San Jose led 3-1 after 40 minutes and had a good chance to extend the lead five minutes into the third, but Luongo kept Vancouver in it with a breakaway stop on Hertl.
The Canucks showed little life until midway through the period, when their new puck-pressure style started to gain them a bit of time in the Sharks zone, but they rarely threatened Niemi's crease.
Vancouver pulled Luongo with 3:08 to go in the period, but Burns scored into an empty net with 2:19 to play.
Down 2-0 after the first period after San Jose goals from Vlasic and Pelech, Vancouver had some pushback in the second.
Canucks captain Henrik Sedin was stopped by Niemi on a wraparound chance, and moments later the Sharks goaltender made a glove save on Daniel Sedin.
Santorelli, with his fourth goal in three games, got the Canucks on the board at 10:20 when he redirected a shot-pass from Vancouver defenseman Ryan Stanton in the high slot past Niemi.
San Jose restored its two-goal lead just 1:35 later when Marleau beat Luongo with a one-timer from the faceoff dot off a setup from Tyler Kennedy and Couture.
Kennedy had a chance to stretch the lead to 4-1 later in the period on the power play, but had his shot ring off the crossbar.
Canucks defenseman Alexander Edler popped Hertl's helmet off as he was reaching for the puck late in the second period.
Vlasic opened the scoring at 12:16 of the first period by finishing off a nice passing play. The San Jose defenseman took a pass from Burns off the rush in the high slot and snapped a shot blocker side on Luongo.
Niemi came up big on a Vancouver power play later in the first, with big stops on both Edler and Jason Garrison.
Luongo then stopped Burns on another good chance before Pelech doubled the Sharks' lead with 58 seconds left in the first.
The 26-year-old nephew of Vancouver general manager Mike Gillis, playing in just his ninth NHL game, chipped a pass from behind the Canucks' net up into the top corner past Luongo.
Earlier in the period, the Sharks hemmed the Canucks in their own zone for two full shifts, forcing Vancouver coach John Tortorella into using his timeout less than five minutes into the game.
Notes: The teams play twice more this season. The Canucks host the Montreal Canadiens on Saturday before heading out on a season-high seven-game road trip. San Jose is home to the Ottawa Senators the same night. ... Canucks right wing Zack Kassian will be eligible to return to the lineup on Saturday after serving his eight-game suspension (three preseason, five regular) after breaking the jaw of Edmonton Oilers center Sam Gagner with a high stick.