The choice made the Hutu leader the most likely ruler of Burundi after his party, the Forces for the Defense of Democracy ( FDD), took 58 percent of last Monday's parliamentary elections.
The FDD, which joined Burundi's power-sharing government in November 2003, said that it had chosen Nkurunziza because his policies would promote reconciliation.
On Sunday, 424 out of 428 FDD delegates from around Burundi voted to support Nkurunziza.
The party of current transitional president Domitien Ndayizeye, the Front pour la Democratie au Burundi (FRODEBU), came out second in last Monday's parliamentary elections, followed by the Parti de unite pour le Progress National (UPRONA).
The parliamentarians and a senate to be elected later this month by communal councils dominated by the FDD will select the president no later than August 19 this year.
The winning candidate needs a two-thirds majority to take over the power in the central African country which suffered more than a decade of civil conflicts between minority Tutsis and majority Hutus.