Sri Lanka were also looking on course to win the second but for an attritional batting effort from Hashim Amla and Johan Botha, who lasted 41 overs to draw the final game, meaning that the hosts won the two match series 1–0.
Sanjeewa Weerakoon took 19 wickets in two games for Sri Lanka A, while opening batsman Avishka Gunawardene impressed with the bat, scoring 207 runs in four innings.
For South Africa, no one individual really impressed, as captain Jacques Rudolph was the top-scorer 149 runs in four innings while Monde Zondeki took nine wickets at an average of 20.77.
Sri Lanka A had put South Africa A in to bat, but conceded 68 runs to the opening partnership of Andrew Puttick and Jacques Rudolph.
Avishka Gunawardene repaired his first-innings duck, making 83 as Sri Lanka A chased down the target with ease - Zondeki getting the best figures again, but this time only one wicket for 27.
South Africa A once again got a good start with the ball, Zondeki getting Tharanga and Ian Daniel out caught, but Lokuhettige once again defied them, as he and captain Gunawardene were batting on the third morning with a slender lead of 127.
Jayaweera, however, was not allowed to bowl, possibly due to the light conditions, and Weerakoon went wicketless as Amla and Botha survived 41 overs and two and a half hours to draw the game.