The Burundian Government and main Hutu rebel group have signed a peace agreement, in an effort to end the country's decade-long civil war.
President Ndayizeye, a Hutu, wants the rebels involved in government
African leaders were present as the deal with the Forces for the Defence of Democracy (FDD) was signed.
But a smaller rebel group - the rebel National Liberation Forces (FNL) - has rejected the accord.
The NLF has been told by the Burundi Government to join peace talks within three months or face the consequences.
ATTENDING THE SUMMIT
Ugandan President Yoweri Museveni
Mozambique President Joaquim Chissano
DR Congo President Joseph Kabila
South African Vice President Jacob Zuma
Ethiopian Prime Minister Meles Zenawi
The African leaders said the FNL would be treated like an organisation which was against peace and stability if it did not join the peace process.
The FNL has said it would only negotiate with members of the minority Tutsi ethnic group - a reference to the Tutsi-dominated Burundian armed forces - and not with President Domitien Ndayizeye, who is a Hutu.
"It is Tutsis who have killed us, and it is with them that we have to negotiate," FNL spokesman Pasteur Habimana said.
But correspondents say the inclusion of the group is necessary for a comprehensive peace.
This week, in the run-up to the two-day summit in Tanzania, 17 people were killed in clashes between government forces and the FNL.
The group is the dominant rebel force around the Burundian capital Bujumbura and can shell the city virtually at will, analysts say.
The conflict between the rebels and the Tutsi-dominated army is estimated to have claimed 300,000 lives in the past decade - mostly civilians.
Burundi's President Ndayizeye and FDD leader Pierre Nkurunziza were joined at the talks by three African heads of state, other senior officials and representatives from the United Nations and European Union.
The protracted war has displaced hundreds of thousands of people
The principal mediators are Uganda's President Yoweri Museveni and South African Vice President Jacob Zuma.
The political and military agreement sets out the details of power-sharing between the government and the rebels.
The signing of the deal ratifies an accord hammered out in October and November in Pretoria, South Africa.