Mubarak Wakaso opened the scoring in the 18th minute with a great goal after Comoro had given away a free kick.
The Black Stars continued to dominate in the game playing much better than they did in the first leg.
Wakaso almost found a brace in the 30th minute as he fired a fierce shot on target, but Abdallah made a good save ensuring that the score remains 1-0.
Gyan also came close to registering his name in the score sheet after a good cross by Andre Ayew, but the captain saw his effort going wide.
In the second half Ghana continued to dominate and pressing hard for another goal.
Comoros saw themselves in a disadvantage as Omarh Mdahomba was shown a second yellow card which saw him walking to the stands.
In the 80 minute Ghana took full advantage as Jordan Ayew pulled a powerful low drive shot, but it was the wood work that denied him the full celebration.
A few minute later Jordan Ayew made it count as he netted inside the box taking the score to 2-0, giving his side a comfortable victory.