There was no immediate confirmation of any charge after England reached 4-192 when bad light stopped play.
Stokes is the latest in a long list of players to have spats with spectators at The Wanderers, where there is a long walk from the dressing rooms to the pitch, alongside a grassy bank often filled with boozy spectators.
A plastic casing was built for the walkway after Australia tailender Merv Hughes swung his bat in anger at a spectator who insulted him in 1994.
Previously it was fenced off, allowing spectators to abutt the walkway and insult players close-up as they walked past.
TV pictures did not show Stokes being insulted but did show him swearing in response to obvious provocation.
Stokes, who has tormented the South Africans with bat and ball on this tour and proved pivotal in England taking a 2-1 series lead, missed the Ashes in 2017 after sustaining a hand injury in a brawl outside a Bristol nightclub which led to him being charged with affray.
He was acquitted after a high profile trial but charged with bringing the game into disrepute by the England and Wales Cricket Board.