The striker fired home on the hour to hand Togo a 2-0 lead in the second leg and 3-1 advantage on aggregate.
Daniel Cousin replied for Gabon to make it 2-1 with 10 minutes remaining but Togo held on at the Stade de Kegue in Lome for a 3-2 final aggregate scoreline. Wome Dove put Togo ahead in the first half.
Ade played a key role in the play-off - he scored Togo's goal in the first leg in Gabon last month.
Togo join 14 other qualifiers and hosts South Africa in the finals in January.
The finalists are - Algeria, Angola, Burkina Faso, Cape Verde, DR Congo, Ethiopia, Ghana, Ivory Coast, Mali, Morocco, Niger, Nigeria, Togo, Tunisia and reigning African champions Zambia.
South Africa qualified automatically as hosts.