de Villiers, who fractured a finger on his left hand during a practice session with the Royal Challengers Bangalore, would under go the operation on Friday.
South Africa team manager Mohammad Moosajee said: "The hand specialist found that AB fractured the hand bone of his middle finger."
"He advised that immediate surgery be done to fixate the fracture and to allow the rehabilitation process to begin as soon as possible."
de Villiers was named South Africa's captain for T20Is and ODIs in June this year and was due to take over from Graeme Smith while Hashim Amla was named the vice-captain.
With de Villiers out of the ODIs, it remains to be seen whether the selectors, who meet next week to pick the team for the Australia series, name Amla as the captain or revert to Smith for just one series.
