The country is now free to compete at next year's Rio de Janeiro summer Olympics under its own flag and plans to send a team of four.
"I am delighted and exhilarated. This will promote reconciliation and national unity," said South Sudan's Olympic chief Wilson Kuoirot.
"Being a member of the IOC will allow us to send a team to next year's Olympics. At present we have four athletes, all training in Kenya."
The unanimous recognition of the country's Olympic Committee drew a loud round of applause from the IOC members with South Sudanese officials visibly moved and some in tears.
"Let me wish you a very bright future," IOC President Thomas Bach said. "We will stand by your side."
"We look forward to welcoming you to the opening ceremony of the Olympic Games of Rio de Janeiro (in 2016). This will put your nation on the world map."
Thousands have been killed and more than 2.2 million displaced since fighting broke out in December 2013 between President Salva Kiir's government and rebels commanded by Riek Machar.
Both sides have been accused of human rights abuses and indiscriminate killings, which have often been carried out along ethnic lines, with Machar's Nuers pitted against Kiir's powerful Dinkas.
South Sudan's marathon runner Guor Marial competed at the London 2012 Olympics but did so under the Olympic flag after refusing to run for Sudan and with South Sudan not yet an IOC member at the time.
He can make amends in Rio as he is part of the four-member team, Kuoirot said.
(Editing by Sudipto Ganguly)
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