William Troost-Ekong’s late winner sent Nigeria through to the semi-finals of the Africa Cup of Nations on Wednesday after a tense 2-1 victory over South Africa in Cairo.

Samuel Chukwueze fired the Super Eagles ahead in the first half in front of a healthy, largely pro-Nigerian crowd at the 75,000-capacity Cairo International Stadium.

But Bongani Zungu’s looping header brought South Africa level on 70 minutes, the goal awarded with the aid of VAR – introduced for the first time at the tournament from the quarter-final stage onwards – after it was initially ruled out for offside.

Centre-back Troost-Ekong then turned home at a corner a minute from time to set three-time champions Nigeria up with a clash against Algeria or Ivory Coast for a spot in the July 19 final.

“We were lucky in the end to score this second goal because in the second half South Africa played much better,” said Nigeria coach Gernot Rohr.

South Africa boss Stuart Baxter admitted the nature of the defeat was tough to digest.

“It’s difficult when you’ve lost a game in the dying minutes, it’s difficult to find positives. I’m sure in one week’s time I will find some positives, but at this moment I’m finding it very difficult,” he said.

Left-back Jamilu Collins made his first appearance in Egypt after shaking off a pre-tournament injury while Villarreal forward Chukwueze came in for Moses Simon in the Nigerian attack.

Baxter stuck with the same side that shocked hosts Egypt in the last round, as match-winner Thembinkosi Lorch retained his place despite Themba Zwane’s return from suspension.

Rohr had suggested South Africa were favourites in the build-up following their defeat of the record seven-time champions, a tag Baxter promptly rejected with Bafana Bafana’s lone competitive win over Nigeria coming in qualifying for these finals.

VAR makes its mark

Odion Ighalo’s goals have been the driving force behind Nigeria’s run here but it was emerging young forward Chukwueze, coming off a solid debut season in Spain’s top flight, who struck just before the half-hour to end the impasse.

Alex Iwobi skipped past a couple of defenders down the left before pulling back for Chukwueze, who swept into the corner as the ball trickled back his way after a first shot was blocked.

Following a stodgy first half Nigeria appeared the far sharper after the break, Peter Etebo rattling the crossbar with a superb 25-yard free-kick.

A number of promising attacks fizzled out for Nigeria and their lack of precision came back to haunt them when Zungu hauled South Africa level, nodding back across goal after a Percy Tau set-piece was shown upon a video review to have been flicked on by Ighalo.

But after their stunning elimination of Mohamed Salah’s Egypt there was to be no follow-up act from South Africa as Williams flapped at an inswinging corner and Troost-Ekong forced over the line with his knee to clinch victory for Nigeria.