It took Australia 18 minutes and 22 balls to claim the last South African wicket when De Kock swung across the line and was leg before wicket to Josh Hazlewood for 83.
South Africa were bowled out for 298, adding five runs to their overnight total of 293 for nine.
The win gave Australia a 1-0 lead in the four-match series.
Just before the rapid conclusion of the match, however, video footage emerged showing Aussie firebrand Warner pointing and directing a verbal barrage at De Kock during Sunday's play at Kingsmead before he was restrained and pulled away by his teammates.
"CA (Cricket Australia) is aware of reports of an incident between players in Durban," a Cricket Australia spokesman said in a statement.
"CA is working to establish the facts of what has occurred and will not be commenting further until that has been done."
The Australians had earlier been criticised for their ebullient celebration of the dramatic run-out of Proteas' star batsman AB de Villiers.
De Villiers was run out for nought after being involved in a mix-up with opening batsman Aiden Markram, with Warner playing a key fielding role in securing the crucial wicket.
In a statement issued by Cricket South Africa on Monday, team manager Mohammed Moosajee said: "It's rather unfortunate that the incident took place and certainly not in the spirit of the game.
"The match referee had spoken to us after the day's play. We will await any further communication from the ICC around this incident."
The Australians' behaviour was slammed by former South African captain Graeme Smith, who told Cricket Australia's cricket.com.au website in Durban that Lyon as an experienced cricketer would "probably say (his action) was unnecessary himself".
"He can be a bit of a fool at times. It's best just to let him be."
The match was effectively won and lost in the first innings when Australia took a lead of 189 runs.
Half-centuries by Warner and skipper Steve Smith and 96 by Mitchell Marsh enabled Australia to make 351.
Early wickets by off-spinner Lyon and a devastating spell of fast reverse swing bowling by Mitchell Starc sent South Africa tumbling to 162 in reply.
The batting of the lower order of the teams was a significant difference.
Australia's last five wickets fell for a total of 166 runs overs the two innings, while South Africa could muster only 27 runs over the same period.
Starc had match figures of nine for 109 and was particularly effective against South Africa's tailenders.
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