The 38-year-old all-rounder announced his retirement from Test cricket in December 2013 after featuring in 166 matches during a 19-year career in the longest form of the game.
Figures of 13,289 runs and 292 wickets helped cement his place as one of the finest all-rounders in the game.
Kallis had targeted a spot in the South Africa team for the Cricket World Cup in Australia and New Zealand next year but described it as "a bridge too far".
However, he will continue to feature for Sydney Thunder and Kolkata Knight Riders in Twenty20 cricket.
"I realised in Sri Lanka that my dream of playing in a World Cup was a bridge too far," he said in a statement on Cricket South Africa's website.
"I just knew on that tour that I was done. The squad that was in Sri Lanka is an amazing one and I believe they have a good chance of bringing the trophy home in March.
"I would like to thank Cricket South Africa, the team, the team sponsors, my sponsors, the fans and all the people who have been involved in my career. It has been an amazing journey.
"I am not retiring from all cricket as I have a two-year contract with the Sydney Thunder and, if possible, [I want] to help the Kolkata Knight Riders defend the IPL title we won earlier this year."
Kallis hit 11,579 runs during one-day internationals for his country, taking 273 wickets.