In the capital, Khartoum, thousands of south Sudanese attacked Arab shops and started fires when news of his death was made public. Police said 24 people died. There were also reports of tension in south Sudan as people gathered to receive news of their leader.
Mr Garang had flown from Uganda to south Sudan on Saturday night after talks with Yoweri Museveni, Uganda's President. Ugandan authorities raised the alarm after they lost contact with the helicopter. Its wreckage was found by local people on the mountainous Ugandan/Sudanese border.
The pilot is believed to have flown into bad weather and lost control of the aircraft. Six of Mr Garang's colleagues and seven Ugandan crew members were also killed. The violence and widespread grief surrounding Mr Garang's death forced most in Khartoum to lock themselves inside their homes. Shop owners shuttered their stores.
"Murderers! Murderers!" yelled some southern Sudanese protesters who alleged the Sudanese government, which had battled Mr Garang's rebel force for two decades before this year's peace deals, may have been behind the crash.
His death is a major blow for the security of east Africa. Kenya had hosted years of peace talks between the warring Sudanese factions and has hosted thousands of refugees from across the border. Uganda had hoped that after the peace deal, Mr Garang would help the Ugandan government end its own war with the rebel Lord's Resistance Army, which used the vast, war-ravaged areas of south Sudan as a base.
Veterans and refugees from south Sudan gathered outside the leader's former home in Nairobi where his group, the SPLA (Sudan People's Liberation Army) and its political wing, the SPLM (Sudan People's Liberation Movement), were based for two decades.
Salva Kiir, Mr Garang's deputy, said: "We want to assure everyone that the leadership and all cadres of the SPLA will remain united and strive to faithfully implement the comprehensive peace agreement." Salva Kiir and other senior SPLA members left for south Sudan yesterday afternoon for emergency talks.
During the civil war, Mr Garang was ruthless in his elimination of enemies within and outside his movement. But when he entered Khartoum for the first time in 20 years on 8 July to become Sudan's Vice-President as part of a deal with the Sudanese government in January, he was welcomed as a peace-maker.
More than one million people turned out to watch him become the first Christian to hold such a senior post in Sudan's Islamic government. Mr Garang and Omar Hassan al-Bashir, Sudanese President, were due to form a government by 9 August. President Bashir said: "We are confident that the peace agreement will proceed as it was planned."
But few believe the south Sudanese process can proceed exactly as planned. "Garang made sure he was the only one who could control the whole of the SPLA and that he was the only one who could deliver a peace deal," said one SPLA source.
Salva Kiir is the likely successor, but Mr Garang's old sparring partner, Riek Machar, is a contender. Mr Machar, who married a British aid worker, Emma McCune, was made governor of the Western Equatoria region but had been sidelined in negotiations.Reuse content