The neighbours agreed in March to resume cross-border oil flows and ease tension that has been permanent since South Sudan's independence in July 2011, following a 2005 treaty which ended decades of civil war.
But the rivals in one of Africa's longest conflicts still dispute much of their 1200-mile border, including ownership of the symbolically important region of Abyei.
Mr Bashir, who cancelled a visit to Juba a year ago when border fighting almost flared into full-scale war, said in a speech in the southern capital yesterday that he had ordered Sudan's borders with South Sudan to be opened for traffic.
"I have instructed Sudan's authorities and civil society to open up to their brothers in the Republic of South Sudan," he said alongside South Sudan's President Salva Kiir.
Mr Kiir said he had agreed with Mr Bashir to continue talks to solve all outstanding conflicts between the African neighbours. "I and President Bashir agreed to implement all co-operation agreements," he said.
Security was tight during the visit to the ramshackle capital which, like the rest of the country, has few paved roads. Police lined main streets, which had been closed and festooned with the flags of both countries.