Pakistan, who recorded a convincing 57-run triumph in the first match, put on board a paltry total of 133 losing all of their wickets in 48.4 overs.
Skipper Sana Mir (35 not out), Javeria Khan (34) and Nain Abidi (21) batted well for Pakistan. Suné Luus bowled lethally and captured a five-wicket haul giving away only 20 runs in her 8.4 overs while Shabnim Ismail took three in her nine overs giving away only 15 runs.
South Africa found tough resistance from Pakistan bowlers especially Anam Amin, who captured four wickets cheaply for nine runs in her ten overs. Kainat Imtiaz took two while skipper Sana took one before South Africa reached the victory total in 48.4 overs. Dane van Niekerk (34 not out) and Trisha Chetty (33) batted well for the winning team.
The two teams will again clash in the decisive third encounter to be played on Tuesday before going into a three-match T20I series.