It was the fifth goal of the season for Stamkos, twice a winner of the Maurice Richard Trophy as the NHL's leading scorer.
Tampa Bay won for the fifth time in six games, getting 25 saves in 26 shots from Ben Bishop. He is unbeaten in his five starts this season.
Tyler Johnson gave the Lightning the lead with a power-play goal in the first period and Mikko Koivu tied it just past the midway point of the third.
Minnesota has lost back-to-back contests following a three-game winning streak. Harding stopped 27 shots in the loss.