Thomas' tally 2:30 into the middle frame gave Florida a 2-1 lead. It was followed 2 minutes later by Jason Garrison's goal on a Panthers power play.
Toronto's Mikhail Grabovski was whistled for slashing 59 seconds later and the Maple Leafs then took another penalty for having too many men on the ice.
Kris Versteeg made the Leafs pay with a 5-on-3 goal that put the Panthers up 4-1.
Erik Gudbranson scored and Jose Theodore turned aside 29-of-32 shots for first-place Florida, which broke a three-game skid.
Grabovski scored twice and Dion Phaneuf added a goal for the Maple Leafs.
James Reimer was lifted in the second period after allowing three goals on eight shots. Jonas Gustavsson entered and stopped 16-of-18 pucks the rest of the way.