There had been speculation that the front-row forward would be replaced ahead of the Springboks' defence of the William Webb Ellis trophy.
But 33-year-old Smit, who led the men in green and gold to a Test victory over the Lions in 2009, will continue to skipper the side, while Victor Matfield is retained as vice-captain.
John and Victor have so much experience and we're lucky to be able to name them as captain and vice-captain," said South Africa coach Peter de Villiers.
"To have both still available in a rugby World Cup year is a great boost.
"History has shown that those teams who do well at World Cups have experience and outstanding leadership and we've learnt that you throw away that experience at your peril."
Smit has led the Springboks in 76 of his 102 caps, including twice against the Lions. He was handed the captain's armband on a permanent basis by Jake White in 2004 and three years later led South Africa to World Cup glory.
"The responsibility comes with a great deal of pressure and expectation but it never loses the thrill or the sense of privilege that comes with it," added Smit.