Two second half goals saw the visitors claim the win.
Nigeria’s Super Eagles fell 0-2 to South Africa in Uyo in a Africa Cup of Nations qualifying match on Saturday.
Tokelo Rantie gave Bafana Bafana a 54th minute lead while Percy Tau wrapped up the result in the 81st minute.
The result makes it the first time South Africa would beat Nigeria in a competitive game in 20 years.
Nigeria now sits in third place of their four-team group – Group E – in the Nations Cup qualifying series.
Libya lead the group after winning 5-1 at home to Seychelles on Friday.
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