The Rangers seemed on their way to regulation-time victory, holding a 1-0 lead with 1:24 remaining in the third period, but the Maple Leafs notched a controversial equalizer.
With Toronto buzzing around the net, New York goalie Cam Talbot appeared to have the puck in his glove as David Clarkson whacked away at it. But the whistle didn't blow, and Nazim Kadri finally poked it into the net.
The Rangers argued vehemently Talbot had frozen the puck, but officials upheld the goal after a video review.
After a scoreless overtime, Stepan and Zuccarello scored in the tiebreaker and Talbot stopped Kadri on Toronto's final try.
Talbot finished with 25 saves as New York close out a franchise-record nine-game homestand with a 3-4-2 mark.
J.T. Miller netted the Rangers' lone regulation goal.
Jonathan Bernier stopped 42-of-43 shots for the Leafs, who dropped to 1-9 in their last 10 road games.