Shortly before a storm broke over the stadium, South African captain Faf du Plessis called up JP Duminy to bowl his off-spinners, and Duminy caught Nasir Jamshed off his own bowling with his third delivery.
Only ten more deliveries were possible before play was halted. Pakistan were 60 for two after 9.1 overs, four runs short of a revised par score after South Africa made 153 for seven in their 20 overs. Jamshed's wicket meant that the target was pushed just out of Pakistan's reach.
Quinton de Kock and Hashim Amla gave South Africa a flying start, putting on 72 for the first wicket before Amla was bowled by Pakistan captain and off-spinner Mohammad Hafeez for 31 off 20 balls.
De Kock made 43 off 33 deliveries before he was well caught at long-on by Sohail Tanvir off Hafeez.
A third wicket fell to slow bowling in the space of 15 runs when Shahid Afridi bowled Henry Davids for three.
The success of the slower men made it puzzling that Pakistan made a late switch in their team, leaving out their world-class off-spinner Saeed Ajmal at the last minute, causing a delay in the toss.
With play starting 25 minutes late following a thunderstorm, Hafeez said it was the first time he had seen the pitch. Ajmal was in the team list handed to the media before the toss but it transpired the change was made as a result of seeing a pitch expected to favour fast bowlers. Junaid Khan, not originally named, took the field instead of Ajmal after Hafeez sent South Africa in.
Hafeez and Afridi took three wickets between them for 39 in their combined eight overs as the South African innings lost momentum.
South Africa's defence of their total started badly when Lonwabo Tsotsobe's first deliveries were called wide, with one going for an extra four runs. But Tsotsobe came back strongly and bowled Ahmed Shehzad for nine in an unbroken four-over spell of one for 19.
Shehzad and Hafeez put on 32 and Pakistan looked well placed before they were thwarted by Duminy and the rain.
South Africa won both Twenty20 matches in the United Arab Emirates last week before the teams travelled to South Africa for a hastily-arranged reciprocal series. A second and final game will be played in Cape Town on Friday before the teams clash in three one-day internationals.