Goals from Samuel Chukwueze and William Troost-Ekong handed the Super Eagles the win, while Bongani Zungu netted Bafana’s consolation goal.
Nigeria secured their place in the 2019 Africa Cup of Nations (Afcon) semi-finals after defeating South Africa 1-0 in a quarter-final match on Wednesday night.
Gernot Rohr made two changes to the team that faced the 2017 Afcon champions Cameroon in the Round of 16 encounter which the Super Eagles won 3-2 on Saturday.
Ola Aina was replaced by fit-again full-back Jamilu Collins on the starting line-up, while Samuel Chukwueze ousted fellow attacker Simon Moses.
On the other hand, Stuart Baxter named an unchanged team with Thembinkosi Lorch, who netted the goal which earned Bafana Bafana a 1-0 win over the tournament hosts Egypt, making his second successive start.
The match got off to a lively start with the two teams searching for an early goal, but they could not keep their shots on target in the opening stages of the encounter.
Nigeria’s midfield maestro Wilfred Ndidi’s powerful long-range shot flew over the crossbar, before Lorch placed his effort wide of the target at the other end.