Togo's victory in Lome ensured progress to the group phase 2-1 on aggregate after a 1-1 away draw in the first leg last Friday.
Tottenham Hotspur striker Adebayor was making his first international appearance since a fatal attack on the team's bus ahead of the 2010 African Nations Cup finals in Angola.
He demanded increased security for the squad before agreeing to return.
Togo were finalists at the World Cup in Germany in 2006 but their poor form in recent years has seen them slip down the rankings and forced to play in the opening knockout stage of Africa's qualifiers for the 2014 finals in Brazil.
Adebayor's country will be joined in the next stage, which kicks off in June, by Congo, the Democratic Republic of Congo, Equatorial Guinea, Kenya, Lesotho, Mozambique, Namibia, Rwanda and Tanzania.
The Democratic Republic of Congo played at the 1974 World Cup finals as Zaire and are also seeking to restore past glories.
Their 5-1 win over Swaziland on Tuesday ensured an 8-2 aggregate triumph.
Namibia recorded an 8-0 aggregate victory over Djibouti after winning 4-0 in Windhoek on Tuesday.
Kenya beat Seychelles by the same score in Nairobi for a 7-0 aggregate triumph while Mozambique won 5-1 overall against Comoros Islands.
Lesotho upset the form book by eliminating Burundi on the away goals rule. The day's biggest upset was an away draw for tiny Sao Tome e Principe.
The former Portuguese colony had not played a match for eight years before Friday's first leg at home to Congo, a game they lost 5-0.
But instead of being on the end of another big defeat in the return in Pointe Noire, Sao Tome held their hosts to a 1-1 draw.
Africa's second round of qualifiers sees 40 countries divided into 10 groups of four. The section winners will progress to the final round of playoff matches in 2013.