The 31-year-old offspinner, who took the key wicket of Travis Head early on before taking 1-46 in his 10 overs, had been making his ODI debut in the 98-run win in Cairns on Tuesday.
But in the match officials' report, concerns were cited about the legality of his bowling action.
With Subrayen now having to face an independent assessment of his action at an ICC-accredited testing facility within 14 days, the news is a blow to the Proteas who are already having to cope without injured star paceman Kagiso Rabada.
After losing the T20I series 2-1, the Proteas are eyeing revenge in the ODI series with two matches still to be played in Mackay on Friday and Sunday.
It was only two months ago that Subrayen also earned his first Test appearance against Zimbabwe in Bulawayo, and he was immensely proud and emotional after the honour of receiving his first ODI cap in Cairns.
Subrayen has previously had plenty of scrutiny over his action, starting well over a decade ago.
In December 2012, Cricket South Africa (CSA) placed him under rehabilitation after two separate independent tests showed his action to be illegal, but he was cleared to bowl again in January 2013 after re-testing.
Subrayen was subsequently reported twice the following two years during matches, before he was eventually cleared to resume bowling after having his action examined at South Africa's national performance centre in March 2016.
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