The win was enough for the Mozambican outfit to annul a 1-2 loss from the first leg and advance 4-3 on aggregate.
Chelito Omar opened the scores after just four minutes before Dayo Domingos Antonio doubled the lead with a header on 22 minutes.
Despite the lead, Ferraviario were guilty of spurning several goal scoring opportunities which could have seen them strengthen their lead.
On 61 minutes, Gil Atoy took the game beyond the visitors with the third goal before Hakim Khamis pulled one back for the Islanders in the closing stages, but it was not enough to boost their chances.
The Mozambicans champions will come up against Barrack Young Controllers of Liberia for a place at the group stage.
Aleixo Fumo (Head Coach, Ferroviário da Beira)
We suffered unnecessarily because we dominated the game and we had the opportunity to achieve a historical result. However, we missed too many chances until the 80th minute, when the opponent scored with the only chance they created. This is football and we have to be serious. This is a moment when we must deal with our football with responsibility. You cannot miss such opportunities like my players did.
Seif Nosar (Head Coach, Zimamoto)
It was a good game. We won 2-1 at home and lost 3-1 in a game which we tried to score the crucial to qualify but the opponent’s goalkeeper denied us. We are eliminated and are sad, but we played two good games against a good team