The Lankans also went on to clinch the ODI series 2-1 and collected some valuable points in the ICC World Cup Super League Tournament.
Debutant Mahesh Theekshana took a wicket in his very first ball after Dushmantha Chameera and Praveen Jayawickrama had struck early as the Proteas were skittle out for 125 in 30 overs.
The 24-year-old left-hander struck 47 from 71 balls with two boundaries before he fell in the 42nd over after Skipper Dasun Shanaka had won the toss and elected to bat first.
Keshav Maharaj, George Linde and Tabraiz Shamsi delivered some crucial blows and at one stage Sri Lanka were in danger of being bowled out for under 200 runs.
However, all-rounder Dushmantha Chameera provided some momentum to the Sri Lanka innings during the latter stages with a useful 29 with the help of three boundaries. (C.D)