Sudan's army said it fought with South Sudan along the disputed border on Wednesday while the South alleged it came under Sudanese air attack, violating a four-day-old UN-imposed ceasefire.
The army in Khartoum said it had expelled South Sudanese troops and their rebel allies from two areas, Kafindibei and Kafia Kingi, in South Darfur state across from the South's Western Bahr el-Ghazal state.
Sudan's foreign ministry has previously described Kafindibei and Kafia Kingi as disputed.
Earlier Wednesday, Southern army spokesman Kella Kueth said Sudan had been "randomly bombarding civilian areas," in the border states of Upper Nile, Unity and Western Bahr el-Ghazal on Monday and Tuesday.
It was not possible to independently confirm his allegation and Sudan has repeatedly denied it has bombed the South.
South Sudan's army confirmed, however, that Kafindibei had been captured by Sudanese troops backed by air support on Monday.
The incident is the first confirmed violation after Khartoum and Juba both pledged to seek peace in line with a United Nations Security Council resolution which threatened sanctions if they did not cease hostilities by last Friday evening.
The UN said the situation along the Sudan-South Sudan border "constitutes a serious threat to international peace and security."
Violation of the UN's resolution came as UN High Commissioner for Human Rights Navi Pillay visited South Sudan to discuss the protection of civilians affected by the border fighting.
While Khartoum announced last week that it would honour the ceasefire, it accused South Sudan of continuing aggression by occupying disputed points along the border and warned that if they did not withdraw they would be forced out in an act of self-defence.
Kueth said his forces were not involved in the Darfur border clashes, saying they were between Khartoum's army and northern rebels.
"We, the South, do not have anything to do with Darfur. We do not concern ourselves about that," Kueth said.
Sudan accuses the South of backing insurgents from Darfur as well as those fighting in Sudan's South Kordofan and Blue Nile states.
Juba rejects the claims, and in turn accuses Khartoum of backing rebels on its territory.
The UN resolution calls on each side to stop supporting rebels against the other.
It also ordered them to pull troops back from their disputed frontier, effective Wednesday, but Khartoum said it could not comply until there was a border agreement.
Both sides are to establish a "Safe Demilitarised Border Zone" and jointly begin monitoring the frontier, the UN resolution said.
South Sudan said it had pulled back its forces in line with the demand.
The UN also requires that by next Wednesday the two countries "unconditionally resume negotiations", mediated by the African Union, on issues left unresolved after South Sudan separated last July following a 22-year civil war.
These include oil payments, the status of each country's citizens resident in the other, disputed border areas and the contested Abyei region.
The resolution followed a border war which erupted between the two nations in late March, culminating in the South's occupation of Sudan's main Heglig oil region and Sudanese air strikes against the South.
Both the air strikes and the occupation were condemned by the international community, which feared the conflict could spread into a wider war.