By Khaled Abdel-Aziz and Katie Nguyen
KHARTOUM/NEW SITE, Sudan, Aug 2 (Reuters) - Northern and southern Sudanese clashed in Khartoum on Tuesday in a second day of violence sparked by the death of ex-rebel leader John Garang who helped end two decades of war in Africa's largest country.
Authorities sent in police and helicopters to quell the clashes. The number of people killed in the capital after Garang's weekend death reached 46, police said.
Garang, leader of southern Sudan's former rebel Sudan People's Liberation Movement (SPLM), died in a helicopter crash.
Some southerners fear his absence could weaken their hand in the country, divided between an Arabised Muslim north and the south, which is a mix of African ethnicities with Christians, animists and Muslims.
"There were some limited clashes in different places in the outskirts of the capital. Police have established control over these areas now," State Minister for the Interior Ahmed Mohamed Haroun told journalists in Khartoum.
Police said the death toll from the violence in Khartoum had risen to 46, but did not make clear if this included new victims from Tuesday's clashes. A security official had said Monday's riots killed at least 36 people.
William Ezekiel, editor of the daily Khartoum Monitor, which has close ties to Sudan's southern community, told Reuters residents reported clashes in outlying areas of the capital.
Two southerners were shot dead by northerners about 18 km (12 miles) north of Khartoum, he said. In the south a church and school were attacked, and 26 people injured in another area. "Today, it is northerners who started (the clashes)," he said.
In some of the worst riots in the capital in years, angry southerners rampaged through Khartoum on Monday, burning shops and vehicles. After a curfew overnight, armoured vehicles were deployed at strategic points around the capital on Tuesday.
In the country's south, grieving relatives and supporters of Garang -- who led their war against the north since 1983 -- paid respects to him around a simple bed in a bush town.
International moves also began to ensure a January peace deal Garang's SPLM struck with the government of Sudanese President Omar Hassan al-Bashir would not unravel.
Two U.S. envoys were on their way to Sudan to encourage a smooth transition in the SPLM to new leader Salva Kiir.
A delegation from Khartoum, led by Federal Affairs Minister Nafie Ali Nafie also went south to pay respects. "We want to affirm here that we will work together with the leadership of the SPLM," Nafie said, standing next to Kiir.
Garang, who three weeks ago became Sudan's vice-president in the peace deal, died when a Ugandan helicopter he was travelling in crashed. There has been no suggestion of foul play.
FIVE DAYS OF MOURNING
Fellow ex-fighters gathered in New Site, a small settlement in the remote bush of southern Sudan, where Garang's body was laid in a wooden casket with a flag. Scented charcoal burned in the modest room where the casket rested.
The SPLM announced five days of mourning and said Garang would be buried in their regional seat Juba on Saturday after his body was taken to other towns in the region for mourning.
Garang's wife Rebecca pleaded for calm. "I accept that God has come to collect him," she told Reuters in New Site. "It is just my husband who has died. His vision is still alive."
The SPLM has moved swiftly to choose Garang's deputy, Kiir, to succeed him. The SPLM expects Kiir to take Garang's post as first vice president in the new power-sharing government set up in the January accord that ended the civil war.
Analysts say Kiir may bring a more collegial style.
"John Garang was a special person, very charismatic and visionary. He was different from Salva Kiir who is calm, composed and calculative," said Kenya's Lieutenant-General Lazarus Sumbeiywo Kenyan, chief mediator of the peace deal.
Washington sent Assistant Secretary of State for African Affairs Connie Newman and U.S. special envoy to Sudan Roger Winter to meet the new SPLM leadership and talk to Khartoum.
The conflict in south Sudan began in 1983 when the Islamist Khartoum government tried to impose sharia Islamic law. Two million people were killed, mainly by hunger and disease.
The peace deal included giving southerners the right to vote on secession after a six-year interim period and shared out Sudan's oil wealth between north and south roughly equally.
Sudan also faces continued civil strife in its western Darfur region, which has killed tens of thousands and forced around 2 million from their homes.