The development ends weeks of deadlock as the main opposition, led by the Forces for Freedom and Change (FFC), and the military agreed to rotate control of the sovereign council - the top tier of power - for at least three years and three months.
According to the African Union (AU), the two sides also pledged to form an independent technocratic government and to investigate the violence of recent weeks, the BBC reported.
The military would lead for the first 21 months, while the opposition will take over for the remaining 18.
Establishing a sovereign council had been one of the main issues that left both parties stuck in a negotiation stalemate in the past weeks.
The FFC said that both sides also agreed to form an independent national commission to investigate the events occurred in Sudan since the ouster of President Omar al-Bashir on April 11.
After the end of Al-Bashir's rule, protesters continued their sit-in outside the military headquarters in Khartoum, saying the new military rulers were a continuation of the former President's regime.
On June 3, the military carried out a violent dispersal on the weeks-long sit-in, leaving, according to the opposition, over 100 people dead.
Government officials put the death toll at 61 nationwide, Efe news reported.
The talks between both parties collapsed after the deadly military crackdown.
The FFC has been since December leading the protests that left Al-Bashir's toppled down after holding power for some 30 years.
Al-Bashir, who took power after he led a coup in the oil-rich country in 1989, was deposed and arrested in a military coup in April that came after months of anti-government demonstrations.
A hike in the price of basic commodities sparked rallies in December 2018, which gathered momentum and spread across the country as thousands took to the streets in a rare display of defiance, calling for the resignation of Al-Bashir.
( With inputs from IANS )