The Bruins forced an extra frame when David Krejci scored with 33 seconds remaining in regulation, but Jeffrey's second goal of the game ended it in overtime, breaking the Bruins' seven-game winning streak.
It was only the fourth win in 14 games for Pittsburgh.
Jeffrey also scored in the second period, Jordan Staal found the net and Marc-Andre Fleury stopped 29-of-31 shots for the Penguins.
Zdeno Chara tallied and Thomas ended with 36 saves for the Bruins.
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