Seam bowler Philander was charged by the International Cricket Council (ICC) after the third day's play in Galle, which ended with Sri Lanka 283-9 in reply to their opponents' 455-9 declared.
A statement from the ICC read: "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.
"The footage, which was not aired during live coverage, was viewed by the umpires after the close of play."
Philander was duly fined 75 per cent of his match fee and accepted the penalty, meaning a formal hearing was not required.
Dale Steyn was the Proteas' most potent bowler on the third day of action, taking 5-50 from 21 overs.
Despite ending the day nursing a hand injury, Steyn was positive about his performance and revealed a confidence flowing through the South Africa camp.
"I'm always attacking the stumps even if I don't always hit the stumps like today," he said.
"There's still always a chance to find the edge of a bat. With every ball, there's always a chance to get wickets.
"We built up a little pressure before tea. There was banter about how the Sri Lankans were not really going anywhere. They had closed shop and I think that became frustrating to them."