An agreement, signed in Addis Ababa on Monday evening, established a joint political and security mechanism, headed by the defence ministers, "to ensure that the two parties can maintain stable and secure relations."
"The agreement also establishes a common border zone between north and south Sudan, which is to be demilitarized and jointly monitored and patrolled," the African Union said on Tuesday, which is mediating negotiations ahead of full independence for the south on July 9.
The news of the accord came 10 days after the northern army occupied Abyei in response to a deadly attack on their troops in the contested border region.
The army's move was condemned by world powers, which have warned it threatens peace between the former civil war enemies.
On Monday, Sudan's vice president Riek Machar agreed with his northern counterpart Ali Osman Taha to form a joint committee aimed at resolving the Abyei crisis.
But Taha rejected southern demands that the army withdraw, saying it would only do so when a political solution had been reached.
Sudan's volatile north-south border runs to more than 2,000 kilometres (1,250 miles), but its demarcation, along with the future status of Abyei, are among the key outstanding issues that the two sides have been struggling to resolve ahead of July.
Some 20 percent of the border has yet to be agreed on.