Cameroon topped the final table with seven points, Burkina Faso edged Cape Verde on head-to-head records for second place after both accumulated four points and Ethiopia were eliminated with just one point.
While Cameroon and Burkina Faso are assured of last-16 places, Cape Verde must wait to see if they go through as one of the best four third-placed teams from the six groups.
In Yaounde, Cameroon broke the deadlock on 39 minutes in a cagey opening half dominated by the two defences.
A free-kick from the Indomitable Lions was partially cleared and Aboubakar rifled a low, left-foot shot through a crowd of players and past goalkeeper Josimar 'Vozinha' Dias into the corner of the net.
Cape Verde reacted to falling behind with a more adventurous approach and troubled the Cameroon rearguard several times before half-time without managing an equaliser.
The island nation introduced Rodrigues for the second half and he equalised within eight minutes through an exquisite back-heel off a low cross that beat goalkeeper Andre Onana.
Aboubakar should have put Cameroon ahead again midway through the second half but blazed over when the ball ran loose inside the box.
In Bafoussam, a city 300 kilometres (185 miles) north west of Yaounde, Burkina Faso went ahead on 25 minutes through Bayala.
After a superb long pass from the centre circle by Adama Guira, Bayala outmuscled two Ethiopian defenders and chipped the ball over advancing goalkeeper Teklemariam Shanko and into the net.
But instead of building their lead, the Burkinabe Stallions conceded on 52 minutes when Ethiopia captain Kebede levelled from a penalty awarded after a VAR review.
Burkina Faso welcomed back captain Bertrand Traore, the Aston Villa forward, after his recovery from Covid-19, but a positive test ruled out goalkeeper Herve Koffi.