The Wayla Antelopes progress 5-0 on aggregate after the victory in Addis Ababa.
A brace each from Shimeles Bekele and Getaneh Kebede and another strike from Omod Okwury helped the home side to the emphatic victory.
The home side dominated the early exchanges and raced into the lead on five minutes with the goal from Okwury.
But the Ocean Stars reorganised their defence and provided stiff resistance until the 62nd minute when Bekele doubled the home side's lead.
The striker made it 3-0 three minutes later before Kebede struck twice in the last three minutes to complete the impressive win.
Ethiopia will now join Group A of the group phase where they will take on South Africa, Botswana and the Central African Republic.
Africa's top 28 nations begin their campaign in June, with a total of 10 four-team groups advancing the winners to the third and final round of qualifying.
In all, Africa will stage 152 qualifiers to determine which five teams will reach the 2014 World Cup.
Five teams will represent Africa at the first World Cup staged in Brazil since 1950.
Ethiopia's World Cup qualifier fixtures:
01-05/06/12: South Africa v Ethiopia
08-12/06/12: Ethiopia v Central African Republic
07-11/06/13: Botswana v Ethiopia
14-18/06/13: Ethiopia v South Africa
06-10/09/13: Central African Republic v Ethiopia