The Tottenham striker, on loan from Manchester City, had been called up by Togo coach Didier Six after he ended his international exile at the end of last year.
But Six told Kenyan just before the game that he still had not linked up with the team, and the ex-Arsenal forward was not present for the game.
"It's always a question mark with Manu. It looks like we'll have to do without him," Six said in a French radio interview ahead of the first round, first leg match in Nairobi.
"It is not a crisis without him.
"This period is a bit tricky. He had a big game with Tottenham against Arsenal on Sunday. There is another very quickly, against Manchester United," added the former France international.
Adebayor had not played for Togo for almost two years after an armed attack on their team bus ahead of the 2010 African Nations Cup finals in Angola that killed two squad members.
But the tall striker made a return last November for the second leg of a World Cup preliminary tie in which Togo beat Guinea Bissau to book a spot in the group phase of the 2014 Brazil qualifiers, which starts in June.