Eto'o nets eighth goal of campaign
It was the second win in five days over the previous group leaders and catapults Cameroon from last place to first in the standings with two rounds left to play.
Olympique Lyon midfielder Jean Makoun opened the scoring in the 24th minute when he diverted a free-kick from Newcastle's Geremi into the net.
Eto'o was quickest to a rebound in the 64th minute after Gabon's goalkeeper Didier Ovono parried a shot from Achille Webo.
Daniel Cousin scored a consolation goal in the final minute but Gabon have now dropped to second in the group on six points, one behind Cameroon. Cameroon next host Togo in Yaounde on October 10.