The Amavubi fell behind in the 40th minute when Gilson Benchimol found the net for the hosts. However, Rwanda responded in first-half stoppage time as Claude Niyomugabo equalised in the 45+2nd minute.
Rwanda completed the turnaround shortly after the restart, with Elie Iradukunda scoring in the 52nd minute to put the visitors ahead for the first time.
The Rwandan side held on to their advantage to claim all three points at the Estádio Nacional de Cabo Verde in Praia.
Match details
• Cape Verde: Gilson Benchimol 40'
• Rwanda: Claude Niyomugabo 45+2', Elie Iradukunda 52'
The result gives Rwanda six points from their opening two matches in Group K, following their 3–1 victory over Liberia in Kigali in the opening round.
Cape Verde, meanwhile, remain without a point after suffering a second consecutive defeat. The Blue Sharks had lost 3–1 to Mali in their opening fixture.
Rwanda’s victory keeps them firmly on course as they pursue qualification for the 2027 AFCON, which will be hosted by Kenya, Tanzania and Uganda.
The top two teams in Group K will qualify for the tournament.