Chandimal was banned by the ICC along with coach Chandika Hathurusingha and manager Asanka Gurusinha for refusing to take to the field for two hours
South Africa already had the series sealed by winning the first three one-day games on this tour.
The 28-year-old became only the third South African batsman to register a hundred in his first ODI.
Chasing 245, the visitors rode on a 91-run partnership between de Kock and Amla, who scored 43, to achieve their target with 7 overs to spare
Sri Lanka's innings lasted just 34.3 overs but batsman Kusal Perera hit a gritty 81 to lift the hosts from a precarious 36-5.
Mathews has been troubled by recurring injuries since being brought back as one-day captain in January and had to sit out some matches
Police said Gunathilaka was not an accused, but a cricket board hearing found him guilty of breaching team discipline
Gunathilaka was quizzed by police about an incident at the weekend when his friend Selliah was accused of raping one of two Norwegian women
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