Shortly before the truce ended at 0400 GMT, fighting was reported in all three of the cities that make up the wider capital around the confluence of the Nile: Khartoum, Bahri and Omdurman.
Sudan's army and the paramilitary Rapid Support Forces (RSF) have been battling each other for more than two months, wreaking destruction on the capital, triggering widespread violence in the western region of Darfur and causing more than 2.5 million people to flee their homes.
Witnesses said army aircraft carried out air strikes in Bahri and the RSF responded with anti-aircraft fire. They reported artillery fire and heavy clashes in Omdurman and ground fighting in southern Khartoum.
Residents also reported clashes near an army camp in South Kordofan State, where a large rebel force that is not clearly aligned with either of the factions fighting in Khartoum has been mobilizing.
The cease-fire was the latest of several truce deals brokered by Saudi Arabia and the United States at talks in Jeddah.
As with previous cease-fires, there were reports of violations by both sides.
Late on Tuesday, both factions blamed the other for a large fire at the intelligence headquarters, which is housed in a defense compound in central Khartoum that has been fought over since the fighting erupted on April 15.
Saudi Arabia and the U.S. said that if the warring factions failed to observe the cease-fire they would consider adjourning the Jeddah talks, which critics have questioned as ineffective.
The conflict in Sudan erupted amid disputes over internationally backed plans for a transition away from military rule following a coup in 2021 and four years after long-ruling autocrat Omar al-Bashir was ousted during a popular uprising.