"This morning, 15 December 2012, the former president underwent a procedure via endoscopy to have the gall stones removed," it said in a statement.
"The procedure was successful and Madiba is recovering," it added, using the clan name by which Mandela is affectionately known.
The 94-year-old is being treated at a private hospital in the capital Pretoria. Initial tests revealed that he was suffering from a recurring lung infection.
"The medical team decided to attend to a lung infection before determining when to attend to the gall stones", the statement from the presidency said.
He was previously hospitalised for an acute respiratory infection in January 2011, when he was kept for two nights.
Mandela has a long history of lung problems dating back decades to when he contracted tuberculosis while in prison.