Chris Higgins also scored for Vancouver and Roberto Luongo made the win stand with 20 saves.
Tye McGinn scored both goals for the Flyers, who dropped to 1-6. The Flyers haven't scored more than two goals in a game this season.
Higgins and Kesler and each scored in the third period to rally Vancouver. The Flyers fell to 1-3 under coach Craig Berube.
Higgins fired a shot off Steve Mason and Kesler pounced to score past the sprawled Flyers' goalie for the winner.
The Canucks tied it 2-2 early in the third when Henrik Sedin fed Higgins for a one-timer and his first goal of the season.
Each team struggled to generate offense. The Canucks failed to crack 20 shots until midway through the third and the Flyers didn't attempt their 20th until the final minutes. The Flyers again failed to score a power-play goal, and their special teams unit ranks among the worst in the league.
Armed with one of the lowest-scoring offenses in the NHL, the Flyers almost broke through early in the first, but Claude Giroux's shot rang off the post. Giroux, once one of the best players in the game, has yet to score this season, though he did pick up his second assist on McGinn's second goal.
McGinn has been impressive since the Flyers brought him up last week. With forwards Scott Hartnell and Vinny Lecavalier out with injuries, the Flyers turned to McGinn and pressed him into service on Giroux's line.
He scored against Detroit in his first game back, then showed against Vancouver that he has a knack for positioning himself in the right place at the right time.
McGinn backhanded a rebound midway through the first for a 1-0 lead.
Philadelphia's lead lasted all of 10 seconds. Mason skated behind the net and tried to clear the puck, but it took a funky carom past him and right to a streaking Kesler, who pounded the puck into the empty net for the easy, tying goal.
McGinn made it 2-1 only 2:10 into the second when he finished off a rush with a poke past Luongo for his third goal of the season. McGinn has a chance to stick around with Hartnell out another two to four weeks with an undisclosed injury.
NOTES: Several Flyers sported pink tape as part of "Hockey Fights Cancer" night. ... The Canucks opened a seven-game road trip, which ends Oct. 25 in St. Louis. ... Sedin scored his 800th career point. ... Vancouver is 3-0 when it allows three goals or less.