Tim Thomas was phenomenal in net, stopping 46 shots in a row after the Flyers took a quick 2-0 lead.
The series now shifts to Boston for the next two games Wednesday and Friday.
Krejci fired a one-timer from one knee that ricocheted off the back off the net and back onto the ice. Play continued until officials could review the call, but the goal was clearly good.
"At first I thought it was in. Then they kept playing," Krejci said.
James van Riemsdyk had a breakout game for the Flyers. He scored two goals and was all over the ice trying to help the Flyers win at least one at home.
Instead, they have to rally from another deficit.
Chris Kelly and Brad Marchand also scored for the Bruins, who have taken a seemingly commanding lead on the Flyers for the second year in a row.
Boston led 3-0 in the East semifinals a year ago before the Flyers won four in a row to advance -- including a rally from a 3-0 hole in Game 7.
Thomas finished with 52 saves.
Brian Boucher, who has won games this postseason as a starter and reliever, couldn't hold off the OT charge. He stopped 21 shots before leaving in the middle of the second after he appeared to hurt his wrist.
It was the fifth time in nine playoff games the Flyers made a goalie switch -- the first because of injury rather than ineffectiveness. The score was 2-2 when Boucher left and when he returned.