The initial agreement would limit the military's formal role to a security and defence council headed by a prime minister, but leaves sensitive issues including transitional justice and security sector reform for further talks.
The deal has already faced opposition from anti-military protest groups and Islamist factions loyal to the regime of former leader Omar al-Bashir, who was ousted in 2019.
Protests broke out in at least two areas of the capital Khartoum before the signing ceremony at the presidential palace, an eyewitness told Reuters.
The military did not appoint a new prime minister since last year's coup, which halted a power-sharing arrangement between the military and the Forces for Freedom and Change (FFC) coalition.
The coup led to more than a year of mass protests against the military and the suspension of billions of dollars in international financial assistance, deepening an economic crisis.
(Reporting by Khalid Abdelaziz, Aidan Lewis, and Nafisa Eltahir; Editing by Gareth Jones)

Sudanese people protest against the military coup in Khartoum, Sudan, 21 November 2021. (Photo: EPA-EFE/STRINGER)