Paceman Steyn has a mild side strain while all-rounder Kallis has a badly sprained little finger.
The pair has been rested in favour of the three-match 50-over series against India which starts next Thursday followed by two tests.
"Dale and Jacques will play a key role in the series against India so we felt it was necessary to take precautionary measures so that they are in prime condition," team manager Dr Mohammed Moosajee said on Thursday.
Pakistan lead the three match ODI series 2-0, their first bilateral series win over South Africa home or away. The greenshirts had beaten the Proteas by 23 runs in the first match in Cape Town and narrowly secured a second win in Port Elizabeth on Wednesday.
Kallis had made a return to the ODI team in the series against Pakistan, having not played ODI's since February, 2012.
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We as of recently have a lesser Inzi ( Maqsood ) in the group, now envision Junior Syed Anwar ( Sharjeel Khan ) that might be great.selectors are you listening ?
We already have a junior Inzi ( Maqsood ) in the team, now imagine Junior Syed Anwar ( Sharjeel Khan ) that would be great.Selectors are you listening ?