Justin Reid-Ross scored a hat-trick to boost South Africa in the play-off for the 11th position.
Malaysia opened the scoring with a field goal by Firhan Ashari in the 26th minute before Reid-Ross hit back in the second half, converting a penalty stroke in the 43rd minute.
Within five minutes, he had converted two penalty corners to complete his hat-trick. Lloyd Norris-Jones, captain Austin Smith and Jean-Pierre de Voux boosted South Africa with a goal each before Malaysia pulled one back in the last minute through Shahrun Abdullah.