Looking tired and wearing a surgical mask, Keita resigned in a brief address broadcast on state television hours after troops seized him along with Prime Minister Boubou Cisse and other top officials.
"If today, certain elements of our armed forces want this to end through their intervention, do I really have a choice?" he said from a military base in Kati outside the capital Bamako where he had been detained earlier in the day.
It was not immediately clear who was leading the revolt, who would govern in Keita's absence or what the mutineers wanted.
Images posted earlier on social media said to be taken at the Kati garrison showed Keita and Cisse surrounded by armed soldiers. Reuters could not verify the authenticity of the videos.
Tens of thousands of protesters have taken to the streets of Bamako since June calling for Keita to resign over what they say are his failures to address worsening security and corruption.
France and other international powers as well as the African Union denounced the mutiny, fearful that the fall of Keita could further destabilise the former French colony and West Africa's entire Sahel region.