Ms Okonjo-Iweala, who negotiated the cancellation of US$30 billion debt to the Paris Club, was switched in June from the Finance
Ministry to Foreign Affairs.
She had remained head of the economics team, but this week was replaced by the new Finance Minister, Nenadi Usman.
President Olusegun Obasanjo had accepted her resignation, which had been prompted by a "compelling need to take care of pressing family issues".
Ms Okonjo-Iweala had clashed with the government after publicly claiming the Nigerian mission in Jamaica had illegally transferred US$4.6 million to the International Seabed Authority - an allegation the government denied.
In a letter accepting her resignation, Obasanjo expressed regret that "the minister had to leave at this stage of our reform programme when various measures adopted by this administration were beginning to yield positive results".
Ms Oknojo-Iweala joined the cabinet in July 2003 when President Obasanjo was returned to office for second term.
She was born in June 1954 and before her appointment into Mr Obasanjo's cabinet in 2003, she was vice president and corporate secretary of the World Bank.