Malaysia rode on an own goal (27th minute) and a second half strike from Firhan Ashari (43rd) to register the come-from-behind victory after Matthew Brown put South Africa ahead in the 13th minute.
After registering narrow wins on opening day, both the teams started the match cautiously, not wanting to risk of falling behind early.
But things started to heat up after 10 minutes when Brown converted South Africa's first penalty corner by slotting the ball high out of reach of Hafizuddin Othman in the Malaysian goal.
Thereafter, Malaysia had multiple chances to take the lead in the final minutes of the opening half but an agile De La Peyre kept South Africa in the hunt as both the teams went into the break locked at 1-1.
Malaysia continued from where they left after the change of ends and took the lead in the 43th minute through Ashari, who blasted the ball into the South African goal after turning around at the top of the circle.