It means the firey left-hander has to cough up $2880.
The ICC cited Warner for making "public criticism of, or inappropriate comment in relation to an incident occurring in an international match".
Speaking on Sky Sports Radio this week, Warner suggested Australia should ask the umpires about the legality of Proteas wicketkeeper AB de Villiers using his glove to "wipe the rough side every ball".
"It was disrespectful for David to publicly denigrate an opponent," said match referee Roshan Mahanama.
"I'm sure David will be careful when making public comments in future."
South Africa coach Russell Domingo on Thursday warned the comments had his team fired up for the third Test which starts Saturday in Cape Town.
While Australian team-mate Ryan Harris attempted to distance his side from Warner's controversial comments.
"I've got no doubt what they did was fine, otherwise the umpires and the match referee would have done something," Harris told reporters.
"They've obviously looked after the ball a lot better than us, and if there's anything illegal about it, I'm sure we would have heard about it by now."