Pakistan pulled off a hard-fought triumph under the Duckworth-Lewis method in a match shortened to 47-overs-a-side at Auckland's Eden Park.
Pakistan's 222 in 46.4 overs, interrupted by two delays for rain, was boosted by 56 from skipper Misbah-ul-Haq while recalled opener Sarfraz Ahmed chipped in with a brisk 49.
De Villiers fought a lone hand in South Africa's 202 in 33.3 overs with a brilliant 58-ball 77 including five sixes and seven boundaries.
Both Pakistan and South Africa now have six points from five matches, behind Pool B leaders India who have a perfect eight from four.
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"I'm not blaming anyone. I'm not saying anyone didn't have the energy. I just didn't feel any electric vibe at the warm-up," said de Villiers.
"That is normally a bit of an alarm bell going off for me. It is my responsibility to try to get the guys going, which I couldn't, so maybe I should take responsibility for that.
"So we need to have a chat about what maybe went wrong tonight and try to get to fifth gear again against the UAE," said De Villiers, of their concluding pool game in Wellington on Thursday.