Jeremy Swayman made 28 saves for the Bruins (47-25-5), who have lost four of six. They had won two in a row entering Thursday.
Boston is fourth in the Atlantic Division, one point behind the Tampa Bay Lightning, and two points ahead of Washington for the first wild card into the Stanley Cup Playoffs from the Eastern Conference.
"They made some plays. Unfortunately, I couldn't come up with the stop," Swayman said. "I just want to make sure I'm doing whatever I can to help this team win. Learned some good things today."
Guentzel gave the Penguins a 1-0 lead at 7:49 of the first period. He took a pass from Sidney Crosby along the blue line while entering the Bruins zone and stickhandled around Charlie Coyle to the slot for a wrist shot.
"I just think he's a great player," Pittsburgh coach Mike Sullivan said. "I think he's quietly emerged as one of the superstars of the League. I think he's one of the best goal-scorers in the League. He shows it year in and year out."
Jason Zucker scored on the Penguins' first shot on goal of the second period to make it 2-0 at 6:10, receiving a stretch pass from Jeff Carter for a breakaway. It was Zucker's second goal in seven games since having core muscle surgery Jan. 25.
Pittsburgh was outshot 10-0 in the period before Zucker's goal.
"We knew they'd be good in the first. They were," Boston coach Bruce Cassidy said. "The start of the second was excellent. We needed a nice play."
Guentzel made it 3-0 at 16:12, shooting from a sharp angle off a pass Kris Letang sent above the crease.
Guentzel completed the hat trick with an empty-net goal from the opposite blue line for the 4-0 final at 17:55 of the third period. The forward has scored 40 goals in 72 games this season, tying his NHL career-high from 2018-19.
"You put a lot of time and effort into this game," said Guentzel, who has scored seven goals in his past four games. "Just to score goals in this league is pretty special. I'm fortunate to play alongside really good players. Just have a good surrounding crew with coaches and teammates and staff, so it's just a cool milestone."