The Black Satellites booked a ticket on a 4-2 aggregate following a 3-1 home victory in the final round first leg encounter.
It is all delight for Jimmy Cobblah's outfit who failed to qualify for the 2017 championship in Zambia, having lost to Senegal at the last hurdle.
In Sunday's fixture, Benin opened the scoring after a goalless first half through Bio Odo Chabi.
Wafa midfielder Prosper Ahiabu, however, restored parity for Ghana with five minutes to play.
The hosts threw everything to cause a last-minute shock but the Satellites held their own to settle for a draw.
Ghana, who accounted for Morocco in the second round of qualifying, join Nigeria, Senegal, South Africa, Mali, Burundi, Burkina Faso and hosts Niger for the final tournament scheduled for February 24 to March 10 next year.
The event will serve as qualifiers for the Fifa Under-20 World Cup to be hosted by Poland later next year.
The Black Satellites, two-time Afcon champions, will be making their 11th appearance at the tournament.