Phehlukwayo and Dwaine Pretorius bowled brilliantly in the death to contain their opposition to 251 runs in 42.3 overs.
Rassie van der Dussen has a batting average of 88.25 in ODI cricket.
The 1996 World champions will not find it any easy after a plethora of changes were made to their squad.
Lasith Malinga will continue to captain the T20I team in the three-match series as an extension to his limited-overs duty.
There is rain predicted throughout the day tomorrow and it wouldn't be a surprise if the game is washed out.
South Africa takes the lead in the 5-match ODI series with a resounding win.
It could be a batting paradise at the SuperSport Park in Centurion.
Oshada Fernando lost an opportunity to make his debut memorable as he had to sacrifice his wicket for Kusal Mendis.
Amla is having a particularly lean phase and averaged less than 24 in 10 Tests before the arrival of Pakistan for a full-fledged tour recently.
Keshav Maharaj picked nine wickets in the previous Test at the venue.