Smith scored a penalty corner with just two minutes remaining to the relief of new head coach Bobby Crutchley.
Julian Hykes scored twice in the first 11 minutes to put South Africa into an early lead before a 13th minute own goal reduced arrears.
Ben Arnold scored his first international goal for England in the 56th minute but the South Africans appeared to have won it when Timothy Drummond converted a penalty corner five minutes from time.
But Crutchley was delighted with his side's determination in Malaysia.
“I thought we battled hard. After a sluggish start we made defensive errors across the pitch, not just in our own circle, and we were punished by South Africa," he said.
"However there were several positive aspects to our play particularly in the second half. I was proud of the team at 3-2 down, we stayed positive and the equaliser was just reward for our resilience throughout the whole game."
England play their second group game against Pakistan on Sunday.