The two sides — representatives from the military council and the Forces for Declaration of Freedom and Change, which represents the protesters — signed a so-called political declaration, one of two documents that are part of the deal, AP reported.
The other document, a constitutional declaration, is likely to be signed within days.
The ceremony took place on Wednesday in the country's capital, Khartoum, and representatives of both sides shook hands.
The signing is a key step in the country's transition after months of street protests that prompted the military to oust autocratic ruler Omar al-Bashir and take over the country in April.