Sudan danger-man Mohammed Abdul Rahman's last-minute goal snatched AFCON qualification from Ghana to hand Sudan a lifeline in the qualifiers.
The MC Algiers forward rose high to connect to a cross in injury time to secure victory for the home side.
The Black Stars began the game brightly, controlling the first 15 minutes but lost steam as the Sudanese took over creating some chances.
Fatau Dauda, who is deputizing for suspended Richard Ofori pulled the save of the half to deny Sudan from taking a first half lead.
Ghana's closest opportunity at goal came when Mubarak Wakaso weaved in a pass but Tariqe Fosu was inches late as goalkeeper Abdallah Ashrin cleared for Sudan.
The Black Stars returned from the break with similar approach they started as Jordan Ayew drew a fantastic save from the Sudanese goalie with a long drive. Ghana had two quick corners which were wasted.
The tides turned again with the Sudanese pushing for an opener, creating chances but the Ghanaian defense were equal to the task, with Djiku and Boye resolute in the heart of defense.
Fatau Dauda produced another timely save to stop danger-man Abdul Rahman from wining a one on one with Djiku.
Abdul Rahman finally broke the deadlock after rising above the Ghanaian defense to connect a cross from the right and grab all three points for the North Africans.
The defeat means Ghana will have to wait for their next game against Sao Tome in Cape Coast to reach Cameroon 2021.