The two sides renewed rivalries for the 20th time in all formats in 2013 and the narrow win gives Faf du Plessis' men their 15th victory after posting 7-153.
Pakistan were 2-60 when the rain brought an end to the contest after 9.1 overs of their response, leaving them five runs short of the revised victory target.
Quinton de Kock (43) and Hashim Amla (31) scored well for the hosts and a slow start from the tourists saw them miss the chance to win the first match of a two-game series.
The wet conditions caused a delay in Johannesburg but South Africa quickly got into their stride when play got under way.
De Kock and Amla put on a 72-run partnership before Mohammad Hafeez (2-25) accounted for them both to leave the home side on 2-81.
Wickets fell at regular intervals as only Du Plessis (22) and David Miller (19) made notable contributions outside the opening pair.
The visitors began their response slowly but after the dismissal of Ahmed Shehzad (9) they began to raise the run-rate through Nasir Jamshed (18) and Hafeez (13 not out).
However, after the first ball of the 10th over the rain returned and play was suspended with Pakistan four runs behind on Duckworth-Lewis.
After 40 minutes of steady rainfall the match was finally called off, handing South Africa a narrow victory.