Harding stopped 21 shots, including 11 in the third period, in racking up his 10th career shutout.
The Minnesota goalie's best save was a sprawling stop on Jakub Voracek late in the game, preserving the Wild's two-goal lead.
Jason Pominville and Charlie Coyle scored less than a minute apart early in the third period, breaking a scoreless tie.
Ray Emery turned aside 19-of-21 shots for the Flyers, whose two-game winning streak was ended.
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