A public decree disseminated on Twitter said Keita named former defence minister Soumeylou Boubeye Maiga to replace Abdoulaye Idrissa Maiga, who resigned unexpectedly on Friday.
Boubeye Maiga is considered close to Keita despite his having to resign as defence minister in 2014 after the Malian army suffered a string of setbacks against Tuareg rebel groups in the country's restive northern region.
The north is still a theatre of unrest almost six years after a French-led military operation chased Islamic extremists linked to Al-Qaeda from a region they had taken control of in early 2012.
The spread of the unrest this year prompted the G5 regional forum, which also includes Mauritania and Chad, to step up peace efforts with French support.
Mali's presidential election is set to take place next year with Keita seeking re-election.