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.
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.
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.
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 play-off matches in 2013.
