Albert Pahimi Padacke handed in his resignation at an audience with Mahamat Idriss Deby Itno, who on Monday was sworn in as "transitional president," Deby's office said.
Deby, a 38-year-old five-star general, took the helm in April 2021 after his father, Idriss Deby Itno, who had ruled for three decades, was killed during an operation against rebels.
Padacke, 55, served for 18 months under the younger Deby.
He had also been prime minister under Deby's father, against whom he ran in presidential elections that took place just before his death.
Deby's junta had originally declared its plan was to restore civilian rule after 18 months in power.
But as this deadline neared, a nationwide forum staged by Deby set a new 24-month timeframe for holding new elections and named him president for the interim.
The conference wound up at the weekend after being boycotted by the main political opposition and two out of the three biggest armed rebel groups.
Promising a "democratic" vote at the end of the transition period, Deby on Monday promised the new government would be formed "in the next few days."