A military band played the national anthems of the two countries as the two heads of state greeted South Sudanese ministers assembled to welcome Bashir.
“There should be peace between the two countries,” he said.
The two nations battled on their un-demarcated border one year ago, with Khartoum’s warplanes bombing the South, and Juba sending troops deep into disputed areas to battle Sudanese soldiers.
The fighting raised fears of wider war with intermittent clashes continuing for several months, but international pressure reined both sides into an uneasy standoff.
But at talks in Addis Ababa in March, Sudan and South Sudan finally settled on detailed timetables to improve relations by resuming the oil flows and implementing eight other key pacts including one for a demilitarised border buffer zone.
Security was tight in Juba with the streets of the southern capital lined with security forces who had started deploying on Thursday night. The only vehicles on the road were official convoys and the few pedestrians moving around were subject to constant security checks.