The Penguins trailed 2-1 after two periods, but Malkin -- marking his return from a four-game absence due to a concussion -- began the comeback with an unassisted goal off a Tampa Bay turnover 5:38 into the final frame.
Steven Stamkos netted his 16th of the season and Tom Pyatt also tallied for the struggling Lightning, who dropped a fifth straight.
Mathieu Garon started in goal for the Bolts but left with an undisclosed injury shortly after helping his team kill off a penalty in the second period, finishing with 12 saves.
Anders Lindback let in two goals on 18 shots in relief.
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