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.

Steven Dishman, 60, went on the run on 28 May 1985 while serving seven years for burglary and theft of property.
He was sentenced in December 1984, and would have been eligible for parole in December 1987.
Dishman was taken into custody by law enforcement officials and the Arkansas State Police.
The inmate escaped from the Cummins Unit in Lincoln County, where convicted murderer Ledell Lee was executed in April.
Solomon Graves, Public Information Officer for the Arkansas Department of Corrections (ADC), said Dishman will have to serve what is left of his sentence.
Further charges may follow in connection with his escape.
According to the ADC website, four prisoners are still at large in Arkansas. Of those, the longest standing escapee is Veal Lee, a thief who went on the run on 15 July 1984.
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.
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An Arkansas prisoner who escaped more than 30 years ago has been recaptured in the city of Springdale, a prisons spokesman said.