Boyes' backhander went through the legs of goalie Josh Harding for the winner. Huberdeau beat Harding on the stick side for the first shootout goal.
Aleksander Barkov scored in regulation for Florida, and Thomas made 31 saves.
Jonas Brodin scored a goal for Minnesota, while Harding stopped 21 shots. The Wild lost their third straight and managed two or fewer goals for the seventh time this season.
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