The Irish won the toss and elected to bat and were bowled out for 166.
Lizelle Lee picked up the best figures of 2/12 while Sune Luus and Dane van Niekerk also picked up two wickets.
The Proteas were on 82/1 before rain stopped play.
Laura Wolvaardt top scored with 32 not out alongside former skipper Mignon du Preez who finished unbeaten on 29.
South Africa, who has already qualified for the World Cup in June, will play India in qualifier tournament finals.
India, Sri Lanka and Pakistan have also booked their spot at the competition.
