The Indomitable Lions, who claimed just a single point from their opening two games and consequently sat bottom of Group A, made it two wins over the same opponents in a matter of five days to go top of the pool.
Cameroon looked in charge throughout the game in Yaounde, and were in front after 24 minutes thanks to Lyon midfielder Makoun.
Inter Milan striker Eto'o then added a second shortly after the hour mark, before Hull City forward Daniel Cousin grabbed an injury-time consolation goal for Gabon.
It was a second win in as many games for new Cameroon coach Paul Le Guen, whose side now have seven points, one more than the Gabonese.
Togo and Morocco are the other sides in the group.