Derek Forsyth's team went down to the Africans for the third time in six weeks after Andrew Cronje and Ignatuis Malgraff confirmed a 2-0 win at the National Hockey Centre at Glasgow Green.
It was supposed to be a day to remember for Grinstead midfielder Ross Stott as he celebrated his 100th cap for the Scots but it ended up being a family disaster as brother Niall was sin-binned for dangerous play three minutes into the second half.
And with Scotland down to 10 men South Africa turned the screw, winning a penalty stroke when Cronje's net-bound strike hit Ross Stott on the shoulder.
Cronje took the stroke himself, slotting underneath goalkeeper Jamie Cachia's despairing reach before Malgraff confirmed the win with a close-range effort late on.
The Scots still have to face the world's number-nine ranked side India on Saturday and then Wales before their final group game with world champions Australia needing at least two victories if they are to make the semi-finals.
That looks unlikely now but centurion Stott is not giving up hope.
He said: "It was a big day for me but it didn't end the way I wanted it to. I was honoured to win my 100th cap but I suppose you can blame the Stotts for the result.
"I didn't think Niall's offence was a yellow card but I suppose the penalty call was correct as it did hit me on the shoulder.
"But we still believe we can qualify. We just need to win our next couple of games, so this is just a minor setback."
Scotland had their chances to avenge those two recent defeats at last month's Investec London Cup but striker Kenny Bain was in particular guilty of some erratic finishing as the former Kelburne frontman wasted five decent chances.
They had little luck with the refereeing calls. William Marshall thought he had fired the hosts ahead after bundling his way into the circle, only for the officials to spot an illegal use of the foot in the build-up.
Wales, meanwhile, are also under pressure after they went down 3-1 to India in their opener.
Rupinder Singh cracked a spectacular strike off the crossbar after six minutes from India's first set-piece chance, but penalty-corner specialist Vokkaliga Ramachandra Raghunath showed his team-mate how it is done as he swept home his 110th international goal a quarter of an hour later from another set-piece.
The Dragons had spent most of the half soaking up Indian pressure but hit back immediately as Andrew Cornick netted from a tight angle.
But the Indians regained their lead eight minutes after the break when Rupinder Singh slammed home from another penalty-corner routine before Gurwinder Chandi tapped home the third.