Bah N'Daw, who also served as defence minister in 2014 and previously headed the air force, has been described by former colleagues as "principled."
Malian officials hope the inauguration will lead the country's neighbours to lift punishing sanctions imposed after the August 18 overthrow of Ibrahim Boubacar Keita as president that have paralysed the landlocked country's economy.
N'Daw, 70, took the oath of office in front of several hundred military officers, political leaders and diplomats. Junta leader Colonel Assimi Goita, 37, was also sworn in as vice president during a ceremony in the capital Bamako.
In his inaugural address, he said he would crack down on graft, one of the main complaints against Keita's government, and stamp out abuses of civilians by the armed forces.
"Mali has been shaken, trampled on and humiliated by its own children, by us," said N'Daw, wearing a long white robe and a blue surgical mask as protection against the coronavirus.
According to a roadmap to civilian rule, an unpublished "transition charter" endorsed by the junta, N'Daw will rule for a maximum of 18 months before staging elections.
"The charter is my guidebook," he declared.
"Mali has given me everything. I am happy to be its submissive slave, willing to do everything for it to return to full constitutional legality, with elected authorities, legitimate representatives," N'Daw said.
"The transition period which begins will not dispute any international undertaking by Mali, nor the agreements signed by the government," he said.
N'Daw, who briefly served as defence minister, also promised to continue a "merciless war" against "terrorist forces and organised crime" and called for a moment of silence to honour fallen troops, Malians, French and UN.
ECOWAS sanctions to stay
The 15-nation ECOWAS bloc took a hard line, slapping sanctions on Mali and threatening a "total embargo" should the junta install military leaders of the interim government.
It stood by that approach on Friday. The president of the ECOWAS commission, Jean-Claude Kassi Brou, declared sanctions "will be lifted when a civilian prime minister is named."
Brou underlined the importance of publishing the junta-backed charter and warned that ECOWAS could not accept that Goita, as vice president, could potentially replace N'Daw.
ECOWAS' "prime concern is maintaining constitutional democracy in the region," he said.
Current restrictions ban commercial trade and financial flows, but not basic necessities, drugs, equipment to fight coronavirus, fuel or electricity.
On Thursday, former Nigerian president and ECOWAS mediator Goodluck Jonathan, had commented favourably on the upcoming swearing-in.
...President of the National Committee for the Salvation of the People (CNSP) and Vice President-Designate, both of who will be taking the oath of office at the official ceremony. We are optimistic that this event will signal the beginning of the return to normalcy in Mali.— Goodluck E. Jonathan (@GEJonathan) September 24, 2020
- GEJ pic.twitter.com/hw6TKvTwq6
"We are optimistic that this event will signal the beginning of the return to normalcy in Mali," he said on Twitter.
Besides fearing that the coup could undermine their own power, presidents in the wider Sahel region are concerned prolonged uncertainty could jeopardise a joint campaign against militants centred in northern and central Mali.
A previous coup in Mali in 2012 helped hasten the fall of the desert north to Al Qaeda-linked militants, forcing a French intervention the following year to drive them back.