Timo Meier scored, and Aaron Dell made 25 saves for the Sharks (17-27-11), who played their first home game since Jan. 18.
"Certainly disappointed with the result, but I really liked our game tonight," San Jose coach David Quinn said. "I thought it was a really good hockey game, fast-paced. I thought both teams were incredibly competitive, both goalies played well, and we just came up on the short end of it."
Rakell gave Pittsburgh a 1-0 lead at 5:52 of the first period. Jeff Petry put the puck on net from the right boards that Dell couldn't control, and Rakell scored on the rebound.
Guentzel made it 2-0 at 11:33 of the second period after Crosby set him up with a no-look pass from behind the net.
"I think we [can be] better," Crosby said. "I think we can possess the puck a little bit more, give teams a little bit less. But that's the consistency that we've got to find here."
Meier cut it to 2-1 at 15:57 of the third period. He skated nearly the length of the ice on the left, held off Penguins defenseman Marcus Pettersson and pushed the puck past DeSmith from just above the crease.
"That's a big-time goal and a power-forward goal," Quinn said. "He's an elite player in this league, and he's a very difficult guy to contain. He had some chances tonight."