A goal in each half was enough for the Black Stars to book a place in the final round of the qualifiers after the homers struggled to completely impose themselves on the game they were expected to easily win.
Wakaso sent Ghana into the lead in the 18th minute with a superbly taken free-kick just on the edge of the 18-yard box to lighten up the mood at the stadium.
This was after coach Avram Grant was forced to make changes following an injury to Jonathan Mensah, introducing Daniel Amartey for the latter.
Soon, captain Asamoah Gyan who was returning to a starting place in the team almost scored with a header from a Andre Ayew cross which inched just wide.
This was the Black Stars clearest chance after midfielder Emmanuel Agyemang Badu darted well for a fine set up, raced deep only to let one fly high and wide from the right side of attack sending both teams into recess with the Stars holding out a slight advantage.
When play resumed, the Stars immediately got a good opportunity to increase the tally after substitute Jeffery Schlupp made a rampaging run on the left to whip a low cross in. Gyan who appeared positioned to latch onto the opportunity hesitated for Comoros to force a clearance to keep the scoreline unchanged.
The tempo of the game suddenly increased and Comoros went on the attack but a great run on the right, and a fine delivery met a poor connection as they chased the game dreaming of a desired upset.
The rain began pouring heavily, affecting play as a result. While Ghana looked for another goal to consolidate their lead, the visitors had a setback to their plan when Ayew got the second goal for the Black Stars.
The striker outwitted his markers and smashed the ball to the top corner of the net for the crucial cushion the Stars needed with 12 minutes to end the match.
Ghana progressed to the next stage of the qualifiers with a 2-0 aggregate over two legs.