The Sovereign Council ruling the country since last year said in a statement Omar died in Juba while taking part in peace talks between his country’s transitional government and rebel groups.
Another statement by the council said the state will hold a funeral in Khartoum for the 59-year old high raking army officer this Wednesday when his body is repatriated.
Omar was member of the Transitional Military Council (TMC) that deposed autocratic leader Omar el Beshir last year in April.
Omar had said on Monday that he was confident the two sides would sign a deal to form a “national army”, state media reported.
Sudan launched in October peace talks with rebel groups in view of stabilizing the country and rebuild the economy and deliver the democracy promises made to Sudanese.
Thousands of people died in the years-old fighting between rebels and army, mainly in the restive western Darfur region.