De Villiers remained part of the 15-member squad, which includes four uncapped players, for the Twenty20 matches in Durban (Dec. 21), East London (Dec. 23) and Port Elizabeth (Dec. 26).
"AB de Villiers remains our first-choice captain in this format," selection convener Andrew Hudson said in a statement.
"But AB is one of the players we need to rotate in the interest of his workload across all three formats and we want to have one captain for the entire series," he added.
For the two-test series against the Kiwis starting on Jan. 2, South Africa stuck with the same squad which beat Australia earlier this month to retain the number one ranking.
Opener Henry Davids of the Titans and the Lions duo of stumper-batsman Quinton de Kock and left-arm spinner Aaron Phangiso were among the new faces in the Twenty20 side.
Lions all-rounder Chris Morris played for the Proteas in a Twenty20 series in Zimbabwe in July but the games were unofficial so he too would fancy winning his first official cap.
"We could not consider JP Duminy, Colin Ingram and Albie Morkel because of injury while we decided to rest Jacques Kallis and Hashim Amla," Hudson said.
Johan Botha was not considered due to his commitments in Australia.
Twenty20 squad: Faf du Plessis (capt), Farhaan Berhadien, Henry Davids, Quinton de Kock, AB de Villiers, Rory Kleinveldt, Richard Levi, David Miller, Morne Morkel, Chris Morris, Wayne Parnell, Robin Peterson, Aaron Phangiso, Dale Steyn, Lonwabo Tsotsobe.
Test squad: Graeme Smith (capt), Hashim Amla, AB de Villiers, Faf du Plessis, Dean Elgar, Jacques Kallis, Rory Kleinveldt, Morne Morkel, Alviro Peterson, Robin Peterson, Vernon Philander, Jacques Rudolph, Dale Steyn.