"The incident that led to the charge being laid took place in the afternoon when Philander was captured on footage changing the condition of the ball by scratching the surface with his fingers and thumb," said an International Cricket Council statement.
"The penalty was accepted by Philander without contest so there was no need for a hearing."
Philander is the second South Africa player to be fined for the offence in the last year after his team mate Faf du Plessis was found guilty of using the zip in his trousers to mark the ball during a test against Pakistan last October.
Philander finished with figures of 0-31 on Friday as a five wicket haul from his fellow paceman Dale Steyn reduced Sri Lanka to 283-9 in their pursuit of South Africa's first innings 455-9 declared.
(Writing by Nick Mulvenney, editing by Greg Stutchbury)
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