The ruling set Mali on a collision course with the 15-member Economic Community of West African States (ECOWAS), which has insisted that the transition, which is due to end with elections in February, remain civilian-led.
After agreeing in October to lift sanctions imposed after the coup against Keita, ECOWAS said in a declaration that the vice president of the transition “cannot under any circumstances replace the president.”
ECOWAS heads of state are due to meet in Ghana on Sunday.
They and Western powers including France and the United States fear the political crisis could exacerbate instability in northern and central Mali, a home base for regional affiliates of al Qaeda and Islamic State.
Goita, a 38-year-old special forces commander, was one of several colonels who led the coup against Keita. He ousted Ndaw after the interim president named a new cabinet that stripped two of the other coup leaders of their ministerial posts.
Late on Friday, Goita said on national television that he would name a new prime minister from among the members of the M5-RFP coalition, which led protests against Keita last year and fell out with Ndaw and Ouane during the transition.
Jeamille Bitar, a member of the coalition, said its pick for the post would be Choguel Maiga, a former government minister.