Craig Kieswetter made 50 off 32 balls with three sixes and three fours in a match reduced by rain to 11 overs per side.
Together with Jos Buttler (32 not out) he put on 48 in 14 balls.
Off-spinner Johan Botha took two for 19 in three overs.
South Africa lead the series 1-0 after their seven-wicket win at Chester-le-Street on Saturday was followed by a no result wash-out in Manchester on Monday.