Bafana Bafana, who are appealing their elimination, thought they had secured tickets to Equatorial Guinea and Gabon after drawing 0-0 with Sierra Leone on Saturday night.
The result left them, the Leone Stars and Niger level on nine points in Group G, with Bafana enjoying a superior goal difference.
However, CAF rules state in the case of stalemate, the team with the best head-to-head ratio prevails, paving the way for Mena's progression.
And Shabba, skippering Bafana in Steven Pienaar's absence, admits the news came as a blow.
"From what we knew, we knew we had qualified, but now we are all disappointed to hear we haven't," he said in the Cape Times.
"It's disturbing that we heard of the rule only after the game," he added.