Amajita won 2-0 in Addis Ababa a fortnight ago.
The visitor’s dictated terms earlier in the game as they tried to reduce the deficit but found the hosts firm in defence.
South Africa was awarded a penalty in the 38th minute after good work from Fagrie Lakay on the right hand side and an Ethiopian defender was adjudged to have handled in the box.
Referee Osiase Koto from Lesotho did not hesitate and pointed to the spot. Ntuli coolly slotted the ball home to give the home side an unassailable 3-0 lead.
Ethiopia nearly got back into the match just a minute before the break, but Dumisani Msibi did well to deny them in a one-on-one situation.
The second half saw the visitors launch a fight back as they enjoyed a greater ball possession but could not show anything for it.
Both teams made several substitutions but that did not change the complexion of the game. Ethiopia nearly found the back of the net had it not been for the great work by Msibi who dived to his left to pull off a great one-handed save.
South Africa brought on Tshepo Chaine, Sikhumbuzo Mazibuko and Bandile Shandu for Pule Maraisane, Siyanda Ngubo and Fagrie Lakay respectively.
Amajita will now face Cameroon in the third and final round of the qualifiers.
The first match will be played on the weekend of 15-17 August while the return leg take place two weeks later on the weekend of 29-31 August.
The winner will qualify for the 19th edition of the African Youth Championships which will be held in Senegal from 8 – 22 March in 2015.
The semi-finalists at the AYC will represent Africa at the 2015 Fifa Under-20 World Cup tournament in New Zealand.
SA U-20: 16-Dumisani Msibi (GK); 2-Madisha Motjeka; 12-Maphosa Modiba; 5-Ayabulela Magqwaka (C); 4-Khumbulani Mkhuze14; 8-Tlotlo Leepile; 18-Siphelele Luthuli; 15-Fagrie Lakay (89th Bandile Shandu); 11-Pule Maraisane (76th Tshepo Chaine); 10-Nhlakanipho Ntuli; 17-Siyanda Ngubo (87th Sikhumbuzo Mazibuko).
Ethiopia U-20: 1-Shifer Wasegida Klilu (GK); 2-Ayele Akiliu Walelegn (C); 6-Reta Andargachkw Yelake; 8-Workv Surafel Gerachew (57th Mohamed Seid Aliyu); 9-Ayalew Behaylu Teshager; 11-Dukele Dawa Hotessa; 12-Tekle Beneyam Tizazu; 14-Alemu Efrem Kere (70th Kebede Qasnake Moges); 15-Tadesse Natnael Zeleke; 20-Kebede Henok Kasahun; 21-Hussen Yared Hassen (55th Desta Melese Tizazu).