Amla has been preferred to Reeza Hendricks, while Lungi Ngidi and Anrich Nortje have been named.
A breakdown of South Africa's probable squad for the 2019 ICC Cricket World Cup in England.
JP Duminy, who scored 76 runs in the series, has jumped from 39th to 32nd spot.
South Africa made a daunting 198 for two and Sri Lanka were beaten by 45 runs according to the Duckworth/Lewis/Stern method when they were bowled out for 137
Reeza Hendricks made 66, his second straight half-century, and captain JP Duminy hit 34 not out off 14 deliveries as South Africa finished the innings strongly.
Malinga said that he would quit one-day internationals after the ICC World Cup 2019 in England and Wales this summer.
Hendricks and Van der Dussen put on 116 off 78 balls for South Africa's second wicket.
Amla, who was rested for the first three ODIs, will make way for Reeza Hendricks, who had originally been left out of the last two games.
Reeza Hendricks and Wiaan Mulder were left out of the South African squad for the fourth and fifth ODI of the Sri Lanka series.
Markram, who has 16 ODIs under his belt, averages 25.43, but his recent two feats have drawn the attention of the South Africa captain.