Bergeron took just two shifts in the second period and did not look comfortable on the ice or on the bench. His final shift was 16 seconds, as he skated off not long after setting up Jaromir Jagr for a shot.
The Bruins announced that Bergeron was taken to a hospital "for observation" but had no other update on his condition.
Bergeron appeared to be in pain as he was bending over on the bench during the second period.
He was not on the bench for the start of the third period, and his absence forced coach Claude Julien to jumble his lines. It helped that rookie Carl Soderberg, who made his playoff debut Saturday night, can play centre.
Blackhawks captain Jonathan Toews also appeared to suffer an injury. He was hit in the head by Bruins defenceman Johnny Boychuk in the second period, then did not take a shift in the third.
Bergeron has been Boston's most consistent forward in the Cup final against the Chicago Blackhawks, especially on faceoffs and defensively. He also recorded nine goals and six assists in his first 20 playoff games.
Bergeron played only 6:06 before leaving the game.