Black Stars hopped to first place in the in Group G with this crucial win on total goals scored after getting tied up on points with the Bafana Bafana boys.
Ghana head into the third and final round of the series where 10 nations will battle it out for five Qatar tickets in a play-off.
Ghana coach Milovan Rajevac made two changes to his starting team, leaving out Joseph Aidoo, whose mistake led to Ethiopia’s equalizer in Thursday’s 1-1 draw.
The Celta Vigo man’s place was taken by Strasbourg center-back Alexander Djiku, who missed the last match due to suspension.
In the absence of injured Arsenal midfielder Thomas Partey, China-based Mubarak Wakaso came into the XI, pushing Ajax sensation Mohammed Kudus further up to No.10 following the latter’s deeper role on Thursday.
Jordan Ayew, meanwhile, moved from the right wing to center-forward, displacing Richmond Boakye-Yiadom to the bench.
South Africa coach Hugo Broos, on the other hand, made three alterations to his first XI, the biggest talking point being the relegation to the bench of dangerman Keagan Dolly.
Also, Israel-based defender Siyanda Xulu made his way back into the starting team after missing Thursday’s 1-0 victory over Zimbabwe due to injury, similar to Royal AM marksman Victor Letsoalo, who led Bafana’s attack on his return to the team after missing the game against Zimbabwe due to suspension.
Teenager Ethan Brooks was a surprise face in the team but Percy Tau’s presence was highly expected.
Requiring a win at all cost to win the group and secure qualification, Ghana started on the front foot, pegging the visitors back into their own half.
In the seventh minute, Kudus sent a free-kick flying over the bar for the first goal attempt of the match, only four minutes before disaster struck as he had to walk off the pitch for picking up an injury.
Having scored twice against Bafana in his previous two games against the side, his withdrawal was certainly a delight for South Africa as it was a big blow to the home side.
On 14 minutes, Jordan had a great opportunity to open the scoring after breaking away from his marker and going one-on-one with goalkeeper Ronwen Williams but the Crystal Palace man hit his shot into the side netting, much to the disappointment of the home fans.
Two minutes later, Ghana spurned another opportunity when substitute Daniel-Kofi Kyereh, having been played through on goal, blasted his shot over the bar after a dangerous ran into the box.
It was all still Ghana at this point, and in the 31st minute, their pressure paid off when Senegalese referee Maguette Ndiaye pointed to the spot after Rushine De Reuk was adjudged to have fouled Daniel Amartey in the box following a corner.
Captain Andre stepped up and expertly sent Williams the wrong way with his kick to put the Black Stars 1-0 up.
After the break, Jordan tested Williams with two separate free-kicks, before Tau called goalkeeper Joseph Wollacott into action at the other end from a free-kick.
Only three minutes later, the Ahly winger made another attempt, beating Baba Rahman to find space for a dangerous run before releasing a shot from outside the box, the effort again handled by Wollacott.
On 78 minutes, Ghana had a glorious opportunity to double their lead when Kamaldeen beat the on-rushing Williams to a through ball but the winger’s attempt to direct a shot into an empty net from outside the box went just wide.
It was a ding-dong affair from this point as the game opened up slightly and a series of half chances would be created, none strong enough to change the score line.
After three minutes of injury time, Ndiaye whistled to bring the game to an end, breaking South Africa hearts and sending the home crowd into a frenzy.
Ghana will have to prepare for a tougher challenge if they must qualify to the global mundial judging from their current form.