Winger Ebo Andoh punished Benin on 20 minutes when he toe-poked a ball from 20-yards atfter wriggling his way through two markers.
The Beninois rarely threatened the Ghana goal area and were booed by the partisan home crowd who were left frustrated by the team's inability to keep possession.
Ghana returned from the break brimming with confidence and piled pressure but winger Acheampong and striker Otoo were wasteful upfront.
Striker Richmond Boakye-Yaidom superbly placed a low grounder that beat the Benin goalkeeper to double the lead.
Ghana are in good stead to secure qualification to next year's finals to be hosted by Libya.
The return leg will be played in Accra on 24 October.
Ghana starting line-up:
Akwesi Frimpong-Bright Addae,Francis Morton, Rashid Sumaila, Karim Alhassan-Afriyie Acquah, James Bissue, Ebo Andoh, Frank Opoku Acheampong-Mahatma Otoo, Richmond Boakye-Yiadom.
Ghana's Under-20 team gave their Africa Youth Chamionship qualification campaign a boost after beating Benin 0-2 in Cotonou in the final round first leg tie on Sunday.
The Black Satellites dominated play from the start and took very little time to unsettle the home side.