More than 1 million people are estimated to have died during the conflict which followed a failed coup attempt in 1966 by army officers from the Igbo ethnic group in southeast Nigeria.
A counter-coup a year later brought a military government to power under Colonel Yakubu Gowon.
Nigeria's first 30 years of independence from Britain in 1960 were punctuated by a series of coups and military rule only came to an end in 1999.
Nigeria still suffers from almost daily violence in the north which stems from ethnic and religious tensions among a population of some 150 million split roughly equally between Muslims and Christians.
Nigerian President Goodluck Jonathan praised Ojukwu, who was 78, as "one of the great personalities of his time who stood out easily as a brave, courageous, fearless, erudite and charismatic leader."
Igbo youths in Ojukwu's southeast homeland flooded the streets chanting "our friend is gone."
"This is a very, very painful loss to me, the Igbo and Nigeria," said Chibuzo Anyanwu, an industry worker in Abia state in the southeast.
"It marks the end of an era and the beginning of a new one for all. His death calls for sober reflections by Igbo and Nigerians on the disadvantaged position of people in the Nigerian nation."
Ojukwu, the son of a wealthy businessman, lost the battle to maintain southeast Nigeria as independent Biafra in a conflict which brought some of the first images of Africans starving to death to Western television screens.
Although Biafrans gained sympathy globally, few countries recognized it as a separate nation and the civil war dragged on until early 1970, mostly as a stalemate.
Nigeria's south-east had recently discovered vast oil wealth and was considered a key region for the unity and development of the West African state.
Ojukwu fled into exile in the Ivory Coast after the civil war but was later pardoned and in 1999 formed the All Progressive Grand Alliance (APGA) party, which he led until his death.
(Additional reporting by Camillus Eboh; Writing by Joe Brock; Editing by David Cowell)