Kallis was the only notable casualty in a 15-man squad for the tournament, to be played at three venues in South Africa from September 11 to 24.
Newly-appointed selection convenor Joubert Strydom said it had been decided not to "sacrifice" Kallis, 31, in the shortest form of the international game.
"It is a long season and he is a key player for us in Tests and one-day internationals," said Strydom.
The South African team, to be captained by opening batsman Graeme Smith, includes veteran opening bowler Shaun Pollock along with a host of largely untried youngsters.
There are only eight survivors from South Africa's squad that reached the semi-finals of the Cricket World Cup in the West Indies earlier this year.
Kallis was criticised for slow scoring during the World Cup.
Among those who did not play at the World Cup are uncapped left-handed batsman Goolam Bodi and brothers Morne and Albie Morkel. Morne is a fast bowler and Albie an all-rounder.
All-rounder Vernon Philander and off-spinner Thandi Tshabalala, who made their debuts on a one-day international tour of Ireland in June, were both picked.
South African squad: Graeme Smith (captain), Goolam Bodi, Loots Bosman, Mark Boucher, AB de Villiers, JP Duminy, Herschelle Gibbs, Justin Kemp, Albie Morkel, Morne Morkel, Makhaya Ntini, Vernon Philander, Shaun Pollock, Thandi Tshabalala, Johan van der Wath.