The designation Commander-in-Chief was given to an individual with ultimate authority over a military force, typically the Head of State of a government. In the time of the Clone Wars, Sheev Palpatine, the Supreme Chancellor, functioned as the Commander-in-Chief for the Grand Army of the Republic. Conversely, General Grievous, the Kaleesh cyborg warlord, possessed the title of Supreme Martial Commander and, as such, served as commander-in-chief for the Separatist Droid Armies during the Clone Wars.
During the Imperial Era within the Alliance to Restore the Republic, Mon Mothma, holding the position of Chancellor, was the one who possessed that title. Despite Darth Vader, a Sith warlord, being formally recognized as a leader when he was later appointed as the Supreme Commander of the Imperial Fleet, he acted as the de facto Commander-in-Chief of the Imperial Armed Forces because he was empowered by Emperor Palpatine.