Neither the Republic nor the Separatists won the Clone Wars. The entire war was orchestrated by Darth Sidious, with the primary purpose of seizing absolute power in the galaxy. In a sense, he and his few loyal supporters (such as Tarkin) were the only winners in the Clone Wars. The Republic was dissolved, democracy disappearing along with it, and replaced by the new Empire, granting Palpatine absolute control. The Separatists were all but wiped out after the deaths of Dooku and Grievous, with the Emperor sending Anakin (as Vader) to kill the remaining leaders on Mustafar.