Nkurunziza took the "oath for a new term of five years", the presidency said in a statement, in a surprise ceremony today, announced only a few hours in advance.
In his oath, the Nkurunziza swore loyalty to the constitution and "to dedicate all my forces to the defence of the best interests of the nation, to assure national unity and the cohesion of the Burundian people, social peace and justice."
His third term has been condemned as unconstitutional by the opposition and provoked months of protests. There have been a string of killings since his reelection, including of a top general, killed in a rocket attack last month.
The ambassadors of European Union nations and the United States did not attend, but were represented by lower ranking officials.
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Nkurunziza won 69.41 percent of the vote, an immediate first round victory.
But the United Nations observer mission said the vote last month was not "inclusive free and credible" and was held "in an environment of profound mistrust" between political rivals.
Burundi's constitution only allows a president to be elected twice - for a total of 10 years in power - but before these polls Nkurunziza argued he had only been directly elected by the people once.
Nkurunziza, a 51-year-old former sports teacher and born-again Christian, was a Hutu rebel leader during the central African country's 13-year civil war, when at least 300,000 people were killed.
The opposition and international community claimed a third term violated the Arusha accords that had brought that conflict, which raged between 1993 and 2006, to an end.
That war pitted rebels from the majority Hutu people against an army dominated by the minority Tutsi.
Top international envoys from the United Nations, African Union, European Union, Belgium and United States have called on all sides to "recommit to a transparent, inclusive, and comprehensive political dialogue".