Chris Kunitz and James Neal scored power-play goals for the Penguins, who had their season-high, five-game winning streak halted.
Marc-Andre Fleury stopped 18 shots for Pittsburgh.
Krejci scored with 1:29 to play, beating Fleury with a wrister from the slot. Chara unloaded the winner from near the middle of the faceoff circles, cutting in from the right point.
Midway into the opening period, Bruins winger Shawn Thornton was given a match penalty for grabbing Orpik from behind, pulling him to the ice and punching him when he was down. Orpik appeared to be dazed, and may have hit his head on the ice.
The Penguins said he was taken to Massachusetts General Hospital where "he is alert and conscious."
Boston's Brad Marchand was injured in front of the Bruins' bench near center ice before Thornton grabbed Orpik.