All-rounder Philander replaces seamer Mthokozisi Shezi in the 15-man touring party as selectors assess their options ahead of the 50-over World Cup to be co-hosted by those two countries early next year.
Fast bowler Kyle Abbott retains his place as Beuran Hendricks, the man he replaced, remains on the sidelines with a long-term injury.
The Proteas defeated Australia and Zimbabwe in the one-day international (ODI) triangular event, a boost for their confidence ahead of the World Cup.
"We are very happy with the progress and momentum the team has established over the last couple of months, first in Sri Lanka and then in Zimbabwe," CSA selection convener Andrew Hudson said in a statement on Tuesday.
"We have another 13 ODIs before we head to the World Cup to round off our preparation."
South Africa will play three one-dayers in New Zealand starting on Oct. 21, before they head to Australia for three Twenty20 internationals from Nov. 5 and another five 50-over matches that begin on Nov. 14.
The squad for the T20 games was also announced on Tuesday with three new caps added to the mix - batsmen Reeza Hendricks and Rilee Rossouw, and emerging fast bowler Kagiso Rabada.
The side will be captained by JP Duminy for the first time, with regular skipper Faf du Plessis rested.
South Africa ODI squad: AB de Villiers (captain), Hashim Amla, Kyle Abbott, Quinton de Kock, JP Duminy, Faf du Plessis, Imran Tahir, Ryan McLaren, David Miller, Morne Morkel, Wayne Parnell, Aaron Phangiso, Vernon Philander, Rilee Rossouw, Dale Steyn.
T20 squad: JP Duminy (captain), Kyle Abbott, Farhaan Behardien, Quinton de Kock, Marchant de Lange, Reeza Hendricks, Imran Tahir, Ryan McLaren, David Miller, Wayne Parnell, Aaron Phangiso, Kagiso Rabada, Rilee Rossouw, David Wiese.
(Reporting by Nick Said; Editing by John O'Brien)
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