Twilight is the only fictional world I know of in which the sole purpose of a werewolf is to protect humans from vampires and kill vampires. Usually werewolf films and vampire films are distinct myths and genres that don’t overlap (save for a few cases like Van Helsing, or Underworld).
Underworld is most relevant to this question since the premise is that vampires and lycans (i.e. werewolves) have been at war for centuries, each trying to annihilate the other. Both these groups are very strong and fights seem to always result in stalemate – I suppose that’s why they’re still fighting.
Whereas Werewolves rely on primal brute strength and stamina in fights, vampires exercise agility and weapons. I think the winner really relies on who is the smarter and more experienced fighter. However
, I personally would put my money on the vampire since werewolves have a slight disadvantage of shifting out of their wolf form and back into their weakened human one.