Owen Tippett scored for the Flyers (27-29-8), who went 0-for-5 on the power play in their third straight loss. Samuel Ersson made 28 saves.
Philadelphia hosts the New Jersey Devils on Saturday.
"We’ve got to keep working at our game," Flyers coach John Tortorella said. "It's going the wrong direction. As each game has gone by, we've gotten worse, so we’ve just got to keep working at our game. We have another chance tomorrow."
The game seemed to turn late in the second period, with the score tied 1-1 and the teams skating 4-on-4. Philadelphia forward Matvei Michkov had a chance from the right side, but Grubauer, lying on his back, made a glove save at 18:16.
On the next shift, Beniers got the puck low in the offensive zone, stepped out from below the goal line and scored to give Seattle a 2-1 lead at 18:57.
"It was a huge save, and in a really timely manner," Beniers said. "And that's what good goalies do -- they make the big saves when it matters most, and that can change the game right there. Could have made it it 2-1 for them, he's able to make that save, we're able to go down and score. Those are big saves in timely moments."
The Kraken made it 3-1 just 41 seconds later with a short-handed goal by Chandler Stephenson, who stole the puck from Sean Couturier at center ice, broke in alone and beat Ersson past his blocker at 19:38.