Right to Dream Academy duo Mohammed Kudus and Ibrahim Sadiq scored to seal the win in the second round return leg fixture at the Cape Coast Sports Stadium.
The Black Satellites have, thus, progressed 2-0 on aggregate following a barren draw in the first leg away tie.
They will face Benin in the third and final round in July, the latter having dispatched Gambia 3-2 after two legs to reach the last phase.
With a shot from outside the box, Kudus broke the deadlock in the 35th minute to send Ghana into the interval with a one-goal advantage.
Just two minutes after the break, club mate Sadiq made it 2-0, dribbling his way into the box before sending the ball pass the goalkeeper.
Seven teams are expected to join hosts Niger for next year's final tournament.
Two-time champions Ghana are hoping to make a return to the U-20 Afcon after failing to qualify for the last edition in 2017.
The 2019 tournament will serve as qualifiers for the Fifa Under-20 World Cup in Poland later next year.