The visitors piled up their highest total against Sri Lanka of 339-5 thanks to brilliant hundreds from Quinton de Kock (128) and AB de Villiers (108) and then restricted the hosts to 257 in 44.3 overs.
Angelo Mathews top scored for Sri Lanka with 58.
South Africa won the first one-day by 75 runs in Colombo while the hosts took the second by 87 in Pallekele.
Scores: South Africa 339-5 in 50 overs: Sri Lanka 257 in 44.3 overs