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.
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.