Still, the Sudanese celebrated in Khartoum and elsewhere across the country Saturday.
Head of the Political Committee at the ruling Sudanese Transitional Military Council (TMC) Yasser al-Atta praised Egypt's role in solving the Sudanese political turmoil.
There will be a new governing council made up of both civilians and generals and the task is to work towards elections within three years.
The agreement was signed by Mohamed Hamdan Daglo, deputy chief of the military council, and Ahmed al-Rabie, representing the Alliance for Freedom and Change protest umbrella, an AFP reporter said.
For several months now since the ouster of Omar Al Bashir, Sudan has been struggling to restore normalcy due to protests waged by the opposition who want the military council out.
The military has ruled the country since it gained independence from Britain in 1956.
People came from outside the capital to join in the celebrations. The names of the members will be announced tomorrow, Sunday.
The prime minister will be tasked to form the government in consultation with the FFC. Subsequently, the military tried to usurp the country's leadership completely, a move that heightened chaos and tensions in Sudan.
Economic woes triggered the initial protests in December.
"Civilian rule, civilian rule", they chanted, promising to avenge the estimated 250 allegedly killed by security forces during the protests.
Former Prime Minister Sadiq al-Mahdi, the leader of the opposition Umma party, said the deal was a "first step" in the democratic change until "fair" elections are held.
The protests broadened into demands for the removal of Mr Bashir - who had been in charge for 30 years.
"Now, thanks to God, I am starting to breathe".
The two sides have agreed to rotate the chairmanship of the council for just over three years. A military leader will head the 11-member council for the first 21 months, followed by a civilian leader for the next 18. The military will also control the defense and interior ministries, which account for a large part of national spending.
Observers have warned that the transitional government will have little leverage to counter any attempt by the military to roll back the uprising's achievements and seize back power.
Thousands of cheering people gathered around the convention hall where the documents were signed, waving Sudanese flags and flashing peace signs. At least nine troops from the paramilitary Rapid Support forces were arrested over the killings.
One of the most immediate diplomatic consequences of the compromise reached this month could be the lifting of a suspension slapped on Sudan by the African Union in June.