The first Vice-President, Salva Kiir, and Second Vice-President Ali Osman Mohammed Taha were in attendance.
The ceremony followed the announcement of the formation of the new government by Bashir on Tuesday, after weeks of heated discussions over key cabinet posts and eight months after the January peace agreement that ended the country's 21-year civil war.
"Dear citizens, I am glad to announce the special presidential decree forming the government of national unity," Bashir said during a special appearance on Sudanese television on Tuesday.
"This government represents good news. It is an expression of the Sudanese people's lively spirit to agree and continue bringing peace and strengthening national unity," he added.
The formation of the new government represents a major step forward in the implementation of the peace agreement signed on 9 January by the Sudanese government and the former southern rebels of the Sudan People's Liberation Movement/Army (SPLM/A).
Of the 29 ministries, 16 remained in the hands of the ruling National Congress Party (NCP). Nine went to the SPLM/A, and the remaining four were divided among various other political parties in accordance with the wealth- and power-sharing quotas agreed to under the Comprehensive Peace Agreement.
The NCP retained the key energy and mining, defence, interior, finance and justice ministries in the new government.
The SPLM/A gained control of the foreign affairs ministry, under senior SPLM/A official Lam Akol, as well as the foreign trade, education and scientific-research, and health ministries.
The government was due to be operational by 9 August, but the death of John Garang, the SPLM/A chairman and former first vice-president of Sudan, in a helicopter crash on 30 July delayed its formation.
The issue of oil also stalled negotiations over the distribution of cabinet positions in the new government, with both the NCP and the SPLM/A trying to secure the strategic energy and mining portfolio, a crucial post in the vast oil-rich country.
Sudan currently has an output of more than 300,000 barrels of crude oil per day and aims to reach the half-million mark by the end of the year.
As recently as 18 September, the new SPLM/A leader, First Vice-President Salva Kiir, stressed the importance of the energy ministry for the south. During a speech in St Matthew's Cathedral in Khartoum, he stated that he was unwilling to relinquish it.
Khartoum newspapers reported on Tuesday, however, that Kiir had decided to give up the struggle in order to hasten the formation of the new government.
Many southerners in Khartoum were disappointed with the outcome, and an unusually large military force - including armoured vehicles and tanks - was present in the town's southerner-dominated suburbs to prevent potential unrest.
A number of major political parties are not represented in the new government, among them the Popular Congress of Islamist leader Hassan el-Turabi and the Ummah party of Sadiq el-Mahdi.
The interim government will remain in place until legislative elections are held in approximately four years. After a six-year interim period, which began on 9 July this year, the south will hold a referendum to decide whether to remain part of a united Sudan or secede.
Meanwhile, Sudanese national radio announced on Thursday that the first vice-president had nominated governors for the 10 states of southern Sudan in accordance with the implementation of the peace agreement.