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The 20-year-old wicketkeeper-batsman replaces Faf du Plessis, who will rest a lower back problem that has also ruled him out of the first four weeks of the Indian Premier League, where he plays for the Chennai Super Kings.
"Faf has been troubled by low back pain over the past while," Proteas team manager Mohammed Moosajee said in a statement released by Cricket South Africa on Tuesday.
"He was recently diagnosed with bony inflammation in the lumbar spine and a six-week rest period has been advised."
De Kock played in three one-day internationals against New Zealand in January, where he kept wicket in place of AB de Villiers.
Although the left-hander averaged only 25 with the bat with a highest score of 31, he is viewed as the long-term successor to De Villiers with the gloves.
South Africa lead the five-match series against Pakistan 2-1 with matches to come in Durban on Thursday and Benoni on Sunday.
(Reporting by Nick Said in Cape Town; editing by Mark Meadows)