All-rounder Kallis was on Saturday omitted from the squad for the Twenty20 world championship, which will be staged in South Africa in September.
The squad which will play three one-day internationals in Zimbabwe next week differs slightly from that selected for the 20-over tournament.
Fast bowler Dale Steyn has been picked in place of all-rounder Justin Kemp, whose wedding is imminent, and wicketkeeper Mark Boucher has been omitted.
AB de Villiers will take over behind the stumps in Zimbabwe.
A Cricket South Africa statement quoted selection convenor Joubert Strydom as saying the squads were similar because South Africa wanted to use their matches against Zimbabwe to prepare for the Twenty20 tournament.
Strydom said Kallis's omission from the Twenty20 squad was due to his being rested.
However, Kallis showed his disappointment by resigning as South Africa's vice-captain and saying he was considering his options for the future.
Boucher supported Kallis in media reports and comments attributed to the wicketkeeper have led to his being summoned to a disciplinary hearing on Friday.
Coach Mickey Arthur said Boucher's omission was not related to this week's rumpus.
"Mark and I had a long discussion about a month ago and we both agreed that with the strenuous season ahead we need to ease his workload on the one hand and on the other hand to give AB more game time with the gloves," the statement quoted Arthur as saying.
The first one-day international will be played in Bulawayo on Aug. 22, with the second and third games scheduled for Harare on Aug. 25 and 26.
Squad: Graeme Smith (captain), Gulam Bodi, Loots Bosman, AB de Villiers, JP Duminy, Herschelle Gibbs, Albie Morkel, Morne Morkel, Makhaya Ntini, Vernon Philander, Shaun Pollock, Dale Steyn, Thandi Tshabalala, Johan van der Wath.
