Evgeni Malkin added an empty-net goal in the final seconds.
The Penguins were the latest team to beat the Eastern Conference-worst Flyers. Off to their worst start after eight games, the Flyers are 1-7 and mired in last place in the conference.
The Penguins outplayed them from the opening faceoff, and nearly doubled the Flyers in shots through two periods.
Jokinen and Kunitz both scored in the second, and Marc-Andre Fleury made it stand with 24 saves.
Wayne Simmonds had the lone goal for the Flyers, who have yet to score more than two in a game this season.
Crosby, who has 29 career goals against the Flyers, has a career-best, seven-game point streak to start the season.
The Penguins grabbed control for good in the second period, taking shot after point-blank shot at Steve Mason. At one point, the Penguins camped out in the Philadelphia zone and held a 20-8 shots advantage. Sprawled on the ice, Mason made two straight fantastic saves against Matt Kiskanen and Deryk Engelland.
Again, the Flyers couldn't generate offense. Matt Read made a sweet steal at the blue line and took off on a breakaway but then whiffed from the circle. He slammed his stick against the boards on his shift change.
The Flyers later failed on three attempts to clear the puck, and Jokinen pounced, scoring his fourth goal of the season for the 1-0 lead. Jokinen scored on Pittsburgh's 22nd shot.
The punchless Flyers didn't attempt their first shot of the second until 10 1-2 minutes in.
Kunitz punched in a rebound with 7:45 left for a 2-0 lead.
Yet, as badly as they were outplayed, the Flyers hung tight. Simmonds screened Fleury and redirected Claude Giroux's shot with 2 seconds left to make it 2-1 and end Philadelphia's 0 for 18 power-play skid.
Giroux has had a miserable season and hasn't scored a goal. As captain, Giroux has taken the public stand that the Flyers can still turn around the season.
"Tonight is going to be a game to bring the fans back on our side and show them we're a good team and can win games," he said after the morning skate.
So much for that.
Crosby's tip-in with 2:32 left for his sixth goal of the season sealed the win.
Giroux hooked Malkin only 1:01 into the game, and the Flyers were whistled for two penalties in the opening 6 minutes. Simmonds misfired on an open net, and Jakub Voracek got cute on an open look and failed on a backhander when he could have flicked in the puck.
The Penguins won 12 of 20 faceoffs in the first, and dominated the rest of the way.
About the only reason for Flyers fans to cheer came in the second intermission when the public address announcer said an assist had been taken away from Crosby. He entered with an NHL-high 12 points (five goals, seven assists). Crosby, though, got the point back.
NOTES: Flyers D Kimmo Timonen sustained a lower-body injury late in the second and didn't return. ... The Penguins have scored at least three goals in every game this season.