The stronger creature won, but...
Godzilla defeated Kong. But let's be honest. This should've been a curb stomp. Godzilla is bigger, stronger, has tougher skin, plates on his back, atomic breath, powerful tail, can breathe underwater, can withstand missiles, and can survive nuclear bombs being detonated on him.
Kong is hurt by bullets. Can punch (but so can Godzilla).
Godzilla should've destroyed Kong with or without his magical ax. But I guess the film has to please the Kong fans too. Oh well.