The Football Federation from the Island wrote a letter to CAF to ask for a withdrawal after they lost the first leg of qualifiers 13-0 on Friday.
Comoros was expected to travel to South Africa next week for the second leg scheduled.
“It is very unfortunate that Comoros had to withdraw from the qualifiers as it is not very good for the development of football in Africa,” Banyana coach Vera Pauw said.
“Even though I understand where they are coming from, I believe coming here to play their match would have been more beneficial for them as they would have learned a few other things.
“But on the other hand I am quite ecstatic for qualifying for AWC in my first stint with Banyana Banyana, and I believe it is something worth celebrating.
“I am really looking forward to the tournament, but we should not forget the bigger picture is to qualify for the Women’s World Cup in Canada. Going to AWC means we are a step closer to achieving that dream.”
Pauw said the withdrawal has not dented her preparation programme.
“Just yesterday we were sitting down mapping the way forward and fine-tuning our programme. Despite the setback of Comoros not coming, we are already looking for a match to play for that weekend because we need to keep the girls active. We will still be in camp regardless,” she added.
The 2014 African Women's Championship will be held in Namibia from 11-25 October.
The tournament is also been used as qualification for the 2015 FIFA Women's World Cup, with the top three qualifying for the finals in Canada.