Kenzo Oshima, Japan's UN envoy and this month's security council president, announced the nomination of the 62-year old career diplomat on Monday.
However, the announcement was overshadowed by North Korea's first nuclear weapons test, which Oshima called "a very serious matter" and "a threat to international peace and security in the region".
Shortly after it formally endorsed Ban by acclamation, the 15-member council returned to closed-door consultations to agree on a response to North Korea's defiance of a council resolution which had urged North Korea not to go ahead with the test.
Ban was the only remaining candidate for secretary-general after six other contenders withdrew following the South Korean foreign minister's decisive victories in four informal straw polls in the council.
Under the UN charter, the 192-member General Assembly elects the secretary-general upon the recommendation of the council.
Oshima said he asked the president of the General Assembly "for prompt steering of the appointment process". The assembly is likely to schedule a vote later this month.
Ban would then take office next January after Kofi Annan, the current secretary-general, steps down after having completed two five-year terms.
Ban has denied that the perception of him as a strong US ally would impede efforts to resolve burning issues such as the Iranian and North Korean nuclear programmes.
He said a good working relationship with Washington was desirable, but on specific issues he pledged to act as an impartial mediator.
"It's really quite an appropriate juxtaposition that today, 61 years after the temporary division of the Korean peninsula at the end of World War II, that we're electing the foreign minister of South Korea secretary-general of this organisation and meeting as well to consider the testing by the North Koreans of a nuclear device," John Bolton, US ambassador to the UN, said.
"I can't think of a better way to show the difference of the progress of those two countries - the great progress in the south and the great tragedy in the north."