Ngidi, 21, made his test debut against the touring Indians in Pretoria earlier in January, taking 6-39 in the second innings for a match haul of seven wickets.
He also played two Twenty20 Internationals against Sri Lanka 12 months ago but missed the ODI series that followed through injury.
Batsman Khaya Zondo, who toured India in 2015 with the side but was not selected, has also been included.
“Lungi has achieved a remarkable double in being named man of the match on both his T20 and test match debuts and he now gets the chance to show what he can do in the 50 overs format,” selection panel convener Linda Zondi said in a statement from Cricket South Africa.
“Khaya has been on the fringes of selection for some time now which included leading the South Africa A side on their recent 50 overs campaign against the England Lions.”
Fast bowler Morne Morkel, all-rounder Chris Morris and leg-spinner Tabraiz Shamsi all return for the series that starts in Durban on Feb. 1.
Faf du Plessis (captain), Hashim Amla, Quinton de Kock, AB de Villiers, JP Duminy, Imran Tahir, Aiden Markram, David Miller, Morne Morkel, Chris Morris, Lungisani Ngidi, Andile Phehlukwayo, Kagiso Rabada, Tabraiz Shamsi, Khayelihle Zondo