Actually, the first people to obtain the Mangekyou Sharingan were Hagoromo Otsutsuki, the Sage of Six Paths, and Indra Otsutsuki, his eldest son. Hagoromo awakened his Mangekyou Sharingan when he stabbed Hamura while he was being controlled. He awakened this before he was even known as the Sage of Six Paths.. After Hagoromo gave birth to Indra, they were the only shown beings to possess a Sharingan, obviously before the Uchiha Clan formed. Indra then killed his two closest followers after the successor of Ninshu was chosen, thus awakened his Mangekyou Sharingan.
Indra awakened his MS after killing his closest followers, Hagoromo awakened his MS (and Rinnegan) after he stabbed a controlled Hamura. This was before Madara and Izuna even existed, let alone the entire Uchiha clan. Thus they were the first to use Mangekyou Sharingan.
Indra and Hagoromo were the first to ever awaken a Mangekyou Sharingan, but why Hagoromo can use his MS abilities (such as susano'o) with his Rinnegan active, yet doesn't possess a Tomoe-Rinnegan is completely unknown.