He replaced all-rounder Ryan McLaren in the side.
Philander had bagged the Man of the Match award in first Test against New Zealand in Newlands before he was ruled out of the second Test match in Port Elizabeth with a hamstring injury. South Africa clinched the series 2-0.
Philander's replacement in the last Test seamer Rory Kleinveldt, and Jacques Rudolph will again provide the bowling and batting cover for the squad.
"We are very happy with the job that Rory did against New Zealand when Vernon dropped out while Jacques provides us with a lot of experience as the cover batsman," Cricket South Africa (CSA) selection convener Andrew Hudson said.
The first Test match against Pakistan will be played at Wanderers in Johannesburg from February 1.
South Africa squad:
Graeme Smith (capt), Hashim Amla, AB de Villiers, Faf du Plessis, Dean Elgar, Jacques Kallis, Rory Kleinveldt, Morne Morkel, Alviro Petersen, Robin Peterson, Vernon Philander, Jacques Rudolph, Dale Steyn.