The Island nation inflicted defeat on the Black Stars at the Felix Houphouet-Boigny Stadium, with goals from Jamiro Monteiro and Garry Rodrigues doing the damage, while Alexander Djiku’s strike only served as a consolation.
Mohammed Kudus and Inaki Williams were both left on the bench, as Chris Hughton made some tough calls in his starting line-up.
Richard Ofori got the nod between the sticks, with Denis Odoi, Alexander Djiku, Mohammed Salisu and Gideon Mensah forming the back four.
Baba Iddrisu partnered with Majeed Ashimeru in a midfield pivot, while Joseph Paintsil and Jordan Ayew started on the right and left flanks, respectively.
Ransford Yeboah Konigsdoffer was also handed his first start in a Ghana shirt following his impressive cameo in the friendly against Namibia, filling the void left by Kudus at no.10, while Antoine Semenyo led the attack.
With the chance to move to the top of Group B following Egypt’s dramatic 2-2 draw with Mozambique earlier in the day, the Black Stars made a sharp start to the game, with Ashimeru nearly setting up Semenyo for an early goal following a marauding down through the middle.
Hughton’s side continued to push and had a penalty call waved away by the referee after Semenyo went down in the Cape Verde penalty box.
A few minutes later, the Blue Sharks also had a penalty shout denied after Djiku appeared to have handled the ball from a swinging cross.
The Island nation seized the moment to get on the front foot and enjoyed the larger share of possession for much of the opening quarter of an hour.
Cape Verde’s dominance finally counted when Ofori failed to parry a long-range shot away from danger, allowing Jamiro Monteiro to pounce on the rebound to score.
The goal sparked the Black Stars into life and they nearly drew level seven minutes later when Mensah put in a low cross but Konigsdoffer couldn’t connect.
Ghana thought they had finally gotten a breakthrough when Ashimeru picked up a loose ball after Yeboah had hit the post with his header, the Anderlecht midfielder firing a thunderous shot into the net from range.
However, the goal was chalked off for offside following VAR review, which showed Konigsdoffer was blocking the sight of the goalkeeper when Ashimeru took his shot.
The Black Stars finally got the equaliser 11 minutes after the restart, Djiku heading home from a Jordan Ayew out-swinger. Although the equaliser shifted momentum onto Ghana’s side, it was Cape Verde who created the better chances in the final half hour.
Ofori had to produce two point-blank saves to keep the scoreline level, first denying Jovane Cabral before again saving Garry Rodrigues’ shot from a one-on-one chance.
Rodrigues would, however, not be denied the second time, with the 33-year-old stealing the headlines by netting the winner in injury time to give Cape Verde a winning start to the AFCON.
The result of the game means the Blue Sharks have moved to the top of Group B, while Ghana sits at the bottom of the group, behind Egypt and Mozambique, who have a point apiece after drawing 2-2 earlier in the day.
Meanwhile, the Black Stars will face Egypt in their next game on Thursday, January 18.