Unwanted by Tottenham Hotspur, the 31-year-old failed to respond to a call-up following a row over the captaincy ahead of Togo's win over Liberia in June.
New captain Serge Akakpo wasted little time in making an impact, scoring after three minutes, before Jonathan Ayite doubled the lead before half-time.
Togo lead Group A with six points.
However, Tunisia will move ahead on Saturday if they record their second victory in as many games when travelling to Liberia.
The game in Monrovia will be the first full international Liberia has hosted since the lifting of a ban imposed because of the Ebola crisis.
Liberia, which last hosted an international in May 2014, was declared Ebola-free on Thursday.
Tunisia beat Djibouti 8-1 during the opening round of 2017 Nations Cup qualifiers in June.
Togo won their second straight 2017 Africa Cup of Nations qualifier when triumphing 2-0 in Djibouti but did so without star striker Emmanuel Adebayor.