Sudan Vice President Ali Osman Taha and South Sudan Vice President Riek Machar issued a report Monday following the end of of two days of talks in Khartoum.
The report states that the two countries will refrain from supporting or harboring armed groups in line with a security deal signed last year.
The countries also agreed to refer their complains to a joint committee, which will investigate the issues, The Sudan Tribune said.
For the first time, the two countries said they will support initiatives designed to bring peace to the two states, the statement reads.
The agreement averted a crisis, as Sudanese President Omar al-Bashir had ordered a shutdown of the oil pipelines that transport South Sudan's crude oil through Sudan's territory after he accused South Sudan of supporting the Sudan Revolutionary Front rebels.
Khartoum officials said the threat would be lifted if an agreement was made within 37 days, the Tribune said.