The game, the second of a two-legged friendly fixture, lacked spark in the first period, with the rare chances only coming from defensive errors.
Nigeria were without top star Perpetua Nkwocha, and her replacements looked lost without her.
They were also missing important guidance from the touchline, with coach Kadiri Ikhana having taken ill and placed on bed rest.
Matters were not helped when captain and goalkeeper Precious Dede took a boot to the chest and was stretchered off early.
An improved second half saw chances aplenty, especially from Desire Oparanozie and veteran Banyana star Portia Modise.
Former African Player of the Year Noko Matlou came on late a fluttered a few feathers.
But in the end, the 0-0 scoreline proved a fair reflection of a game that never even threatened to bear fruit.
Nigeria: Precious Dede, (Tochukwu Oluehi 15'), Joy Jegede (Osinachi Ohale 83'), Gladys Akpa, Evelyn Nwabuoku, Ngozi Ebere, Esther Ohadugha, Gloria Iroka, Stella Mbachu, Esther Sunday, Ameze Aighewi (Ebere Orji 46'), Desire Oparanozie.
South Africa: Roxanne Barker, Lebogang Mabatle, Nothando Vilakazi, Amanda Sister, Andisiwe Mgcoyi, Zamandosi Cele, Kylie-Ann Louw, Amanda Dlamini, Portia Modise (Matlou 68'), Gabisile Hlumbane (Leandra Smeda 67'), Nocawe Skiti.