Nkurunziza won 69.41% of the vote in Tuesday's election, said Pierre Claver Ndayicarie, head of the electoral commission.
Scores died in pre-election violence
, with protesters arguing that a third term was prohibited by a peace accord that ended a 1993-2003 civil war. Demonstrators rallying against Nkurunziza's candidacy were met with deadly force by police.
Nkurunziza will now continue to rule over a country that has seen months of chaos in the lead up to the presidential elections.
In April, Nkurunziza announced he would run for a third term. The subsequent unrest left scores dead and forced more than a 170,000 people to flee the country.
In May, Nkurunziza held onto the Burundian presidency after a failed coup attempt by an army general while Nkurunziza was in Tanzania. Burundian authorities said they had arrested the general and others involved in the attempt after Nkurunziza returned.
In the days following the coup attempt, an opposition leader, Zedi Feruzi, was assassinated, gunned down in a drive-by shooting alongside his bodyguard in Bujumbura, the capital of Burundi. Opposition parties suspended their dialogue with Nkurunzinza's government after Feruzi's death and the continuing violence throughout the country.
More people died in various attacks and in confrontations between police and protesters that spanned the pre-election period. Belying the chaos of the situation, the military occasionally became
a buffer of sorts between police and protesters. Troops reportedly urged police not to fire live rounds on protesters.
Protests and violence continued to grip much of the country, and the turmoil continued on through the election. Scattered gunfire could be heard in the streets of the capital, Bujumbura, as voters cast ballots after polling stations opened.
At least 17 opposition parties
refused to participate in the elections. Many observers from outside Burundi were vocal in their criticism of the election proceedings as well. Among those to question the legitimacy of the elections was the United States.
On Tuesday, Rear Adm. John Kirby, a spokesperson for the State Department, said in a statement, "The United States warns that elections held under the current conditions in Burundi will not be credible and will further discredit the government."
Kirby went on to criticize what he called the Burundian government's "harassment of opposition and civil society members, closing down of media outlets and political space, and intimidation of voters."
As Nkurunziza prepares to begin the third term his government claims he has won, many fear the turmoil of the past few months may not be over soon. Some refugees and observers worry that it is the beginning of another civil war. The last civil war, categorized by some as an ethnic conflict between Hutus and Tutsis, left 300,000
The small, lush nation in central Africa has a population of almost 10.4 million.