While Bafana Bafana and Libya shared the spoils in Durban, Nigeria got their first win in Group E by thrashing the Seychelles.
Gernot Rohr's charges needed a return to winning ways in the group after the Super Eagles suffered a defeat to Stuart Baxter's charges in the opening game on home soil.
The visitors broke the deadlock after just 14 minutes thanks to a thumping effort from Ahmed Musa after the winger latched onto a knockdown from Odion Ighalao.
Rohr's men doubled their lead 10 minutes before the break as when Chidozie Awaziem slotted home from close range after Kelechi Iheanacho's free-kick crashed against the woodwork
The visitors managed to bag their third goal 10 minutes into the second stanza, with Ighalo converting a penalty, which also proved to be the final goal of the game.
Following Saturday's matches, Libya remain top of Group E, level on points with Bafana, while Nigeria and Seychelles sit in thrid and fourth respectively.