Zuma, 73, went into hospital for the scheduled procedure on Saturday after the gallstones were discovered during a routine check-up two months ago.
“President Jacob Zuma has been discharged from hospital where he underwent a successful procedure to remove gallstones last night,” the presidency said in a statement.
“Doctors are pleased with the outcome of the operation. The President will spend the next few days resting and recuperating at home. He will also work from home during this period.”
Zuma is in generally good health but was briefly admitted to hospital last year suffering from exhaustion after elections won by his ruling African National Congress.
The president, who has four wives and more than 20 children, was a fellow anti-apartheid prisoner on Robben Island with Nelson Mandela before becoming president in 2009.