The Black Stars were close to gaining a point till Sudanese danger man Mohammed Abdul Rahman dragged a dagger through the hearts of Ghanaians with a header in the dying embers of the game.
Ghana started the game brightly in the opening first quarter but did not trouble the Sudanese goal for all their early dominance.
It did not take long as the home side took over and controlled proceedings with Fatau Dauda chosen to start ahead of Ati Zigi pulling off the save of the first half after denying the Sudanese with a smart stop.
There was some half chances for Ghana as Mubarak Wakaso fresh from lifting the Chinese Super League with his side Jiangsu Sunning sent an outstanding pass to Tariq Fosu but he was late as the Sudanese goalkeeper rushed out to clear the danger.
Jordan Ayew also tried his luck from distance with a fierce shot but was saved by the Sudan goalie Abdallah Ashrin as Ghana wasted the resulting corner kicks that came their way in the second half.
The Nile Crocodiles regained control of the game and created several chance but were thwarted in their efforts by the center back pairing of John Boye and Alexander Djiku who kept the Sudanese at arms length.
Sudan nearly took the lead as MC Algiers forward and danger man Mohammed Abdul Rahman tussled with Alexander Djiku before Fatau Dauda intervened.
But it did not take long as Mohammed Abdul Rahman broke the deadlock after connecting with a cross from the right flank to send the stadium agog as the Sudanese scored deep in injury time.
The defeat has now postponed Ghana's chance of reaching the 2021 AFCON in Cameroon till they play against Sao Tome and Principe at home.