The tournament champions, first runners-up and second runners-up will in turn qualify for the Africa U17 Cup of Nations (Afcon) in Morocco later this year.
Konate opened the scoring for Cote d Ivoire in the ninth minute, the effort lasting as the only goal until the end of the first half.
Just two minutes after the break, Miezan guided the ball into the net to double the lead.
In the 51st minute, Ghana halved the deficit as Batigi beat Cote d Ivoire goalkeeper Issa Fofana.
Emmanuel Don, however, restored the Ivorians lead, converting to make it 3-1 after Togolese referee Vincentia Enyonam Amedome pointed to the spot.