Jonathan, wearing his customary wide-brimmed hat, put on a sash bearing the national colours of green, yellow and white, signifying that he had formally taken office. He said his priorities would be peace in the oil-rich Niger Delta, electoral reform and the fight against corruption.
There is uncertainty over whether the ambitious Jonathan will bow to pressure to step aside when presidential elections are held next year.
The death last night of Yar'Adua, who was 58, did not come as a surprise. He had long suffered from kidney ailments and was recently hospitalised in Saudi Arabia because of heart inflammation.
He is due to be buried before sundown today in a Muslim ceremony in his home state, Katsina. Nigeria has begun seven days of national mourning.
Barack Obama led tributes from world leaders, praising Yar'Adua's "profound personal decency and integrity" and his "passionate belief in the vast potential and bright future of Nigeria's 150 million people".
Nigeria's main militant group, the Movement for the Emancipation of the Niger Delta (MEND), said it was saddened by Yar'Adua's death. "MEND considers the late president a genuine peacemaker whose initiatives, humility and respect began to bring confidence to the peace process," the group said. "His death may leave a vacuum that may not be filled."
Jonathan said Yar'Adua left a "profound legacy" for him to follow, adding: "He was not just a boss, but a good friend and a brother."
It is almost three months since Jonathan assumed control of Nigeria as acting president. He appointed a new cabinet and his own team of advisers, but significant policy changes are not expected.
Taking the oath of office in front of ministers, state governors and ambassadors in Abuja today, Jonathan said: "Our total commitment to good governance, electoral reform and the fight against corruption would be pursued with greater vigour. One of the true tests will be that all votes count and are counted in our upcoming presidential election."
He said peace in the Niger Delta, home to the country's oil industry, remained a priority. Attacks by militants there last year crippled oil production. Yar'Adua had tried to end the insurgency peacefully, but those efforts frayed due to his worsening health.
Jonathan will now appoint a vice-president and the pair will complete the unexpired presidential term until elections due by April next year, likely to be the most fiercely contested since the end of military rule. It is unclear whether Jonathan, who is from the southern Niger Delta, will run for president. There is an unwritten agreement in the ruling party that power alternates between north and south.
Kayode Akindele, a director at the Lagos-based consultancy Greengate Strategic Partners, said: "The paramount issue will be who the new vice-president will be. It'll probably be a northerner who will be frontrunner for the presidency in 2011."
Jonathan, a marine biologist, wore the traditional black clothes of the Niger Delta region to his inauguration. He remained seated during Muslim prayers offered on Yar'Adua's behalf, but stood for a Christian invocation.
The country remains volatile and plagued by corruption, but regional analysts said they did not expect Yar'Adua's death to threaten stability. Antony Goldman, head of the London-based PM Consulting, said: "I think Nigeria is better placed to absorb the impact than on previous occasions. I don't think this comes as a shock to too many people in Nigeria or outside the country."
He added: "The issue now isn't over the immediate handover but the implication it has ahead of elections. Nigeria looks ahead to next year's election with a much more open field than has been the case in the past."
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