Garangs death in a helicopter crash last week, which sparked three days of rioting across Sudan that left at least 130 people dead and hundreds injured, raised concerns that the peace deal that ended the countrys 21-year civil war was in danger of unravelling.
Still, Salva Kiirs swearing-in could mark a change in the long-term direction of the peace process between the Khartoum government and Garang. The charismatic Garang favoured a unified Sudan, a position that undoubtedly pleased officials in Khartoum, but distanced him from the vast majority of ordinary southern Sudanese as well as most of SPLMs top officials, including Salva Kiir.
Salva Kiir and Sudanese President Omar al-Bashir used the occasion of Garangs funeral in the southern town of Juba to reassure the shaken country that they would not veer from the peace process that Garang worked so hard for.
The January peace deal calls for a unity government to share power and oil revenue between the north and the south, and gives southerners the right to decide whether to remain part of Sudan or secede after a six-year interim period.
"Im optimistic under the circumstances that the deal is done and it is recognized internationally," said United States senior envoy to Sudan, Roger Winter, after meeting with Sudans second vice president Osman Ali Taha.
Garang's support for a unified Sudan stemmed partly from his belief that he could win a national election to become the countrys first African president.
But Salva Kiir, lacking Garangs charisma, will be hard-pressed to maintain unity within his own rebel movement, analysts say.
Many southern Sudanese fear that Salva Kiir, lacking Garangs stature and charisma, could cave-in to the demands of the Khartoum government.
"Here is a military man and hes going to have to mold himself into a statesman. Hes going to have to make changes in his desire for a separate state to please Khartoum," said David Dagu, 24, director of South Sudan Youth and a member of the SPLM, echoing the sentiments of many southern Sudanese.
Still, months before Garangs death, cracks began to emerge in the SPLM leadership.
In the days leading up to the final January peace deal, rumours spread within the ranks of the SPLM that Garang was about to arrest Salva Kiir, his close friend and longtime deputy, who had to barricade himself at his headquarters in Yei in southern Sudan.
Apparently, Salva Kiir had expressed dissatisfaction with the widening gap between himself and Garang, who also seemed to be increasingly at odds with other SPLM leaders.
Like many African heads of state, Garang was an autocratic leader who often jailed or exiled members of his rebel movement who challenged his authority.
"When [Garang] leaves for abroad, no directives are left and no one is left to act on his behalf," said Salva Kiir, in a December 2004 meeting of SPLMs top commanders, the minutes of which were published this week in The East African, a regional weekly paper.
"Does he carry [the movement] in his briefcase?" asked Salva Kiir.
In mid-July, less than a week before his death, Garang dissolved his rebel leadership and appointed a caretaker government to steer southern Sudan through the six-year interim period, as stipulated in the January peace agreement. The move sparked tension among SPLM commanders, many of whom had been phased out of leadership positions within the rebel movement.
Rebel soldiers were ordered on high military alert the day Garang arrived in Rumbek, the souths provisional capital, to announce the new government, several SPLM sources said.
Angry southern Sudanese suspicious of foul play in Garangs death sparked last weeks violence, which prompted swift retaliatory attacks by northerners. The violence underscored the lingering distrust between the communities and sent a message to the countrys leaders: Peace deals made in the corridors of power dont necessarily translate to peace on the ground.
Fuelling the hostility are the cultural and religious divides between Sudans Arabized Muslim north and mostly Christian and animist south.
"Africans and Arabs are bound to live together," said Jan Pronk, the United Nations envoy to Sudan.
As southern Sudans top official, Salva Kiir will have to help southerners overcome significant psychological barriers before the eventual merging of the two communities.
Many towns in southern Sudan, including the souths provisional capital of Rumbek, have driven out their Arab populations who are seen as benefactors of an Arab-dominated government that sought for more than two decades to destroy the south.
In Juba, one of the few government strongholds in the south, southern Sudanese youth looted and destroyed the town's mostly Arab-owned market. At least 13 people were killed there in two days of rioting, according to the Sudanese Red Crescent.
Hundreds of Jubas Arabs fled to the relative safety of Khartoum.
Across southern Sudan, Arabs have fled to the north. Despite the January peace deal and its promise of stability, they have yet to return. Many southern Sudanese are doubtful they ever will.
"We don't want to do any more business with the Arabs. The only thing the Arabs did here was run the shops that took our money," said Mabor Chawwup, Rumbeks mayor. The market in Rumbek is now run mainly by ethnic Dinkas, Garang's tribe.
Its a position that Salva Kiir could have supported as Garangs deputy, but not as the countrys senior vice president.