Anya Shrubsole, Heather Knight and Jenny Gunn each took two wickets to limit South Africa to 101-7 in Chennai.
England raced to their target with 3.3 overs to spare thanks to Sarah Taylor's 37 off 36 balls and Amy Jones' 28.
England, who beat New Zealand in their first two practice matches, begin their World T20 campaign against Bangladesh in Bangalore on Thursday.
India get the tournament under way against Bangladesh in Bangalore on Tuesday, before New Zealand face Sri Lanka in Delhi.
The men's competition also starts on Tuesday, when India play New Zealand in Nagpur.
England sealed a third win in three World Twenty20 warm-up games, thrashing South Africa by seven wickets.