After winning the first leg 3-0 in Lubumbashi last weekend, the Congolese side lost 1-0 on Sunday evening at the Mandela National Stadium, on the outskirts of the Ugandan capital Kampala to qualify 3-1 on aggregate.
"We are happy to qualify for the next stage. The boys played according to instructions," CS Don Bosco's Coach Lamine Ndiaye said after the match.
After a dull first half, SC Victoria University returned looking hungry for goals and with the introduction of Daniel Isiagi Opolot, they put the visitors under lots of pressure.
With 11 minutes to full time, the 18-year old Isiagi released Isaac Muleme on the left, and the Cranes winger made no mistake delivering a good cross that Matthew Odong sent past goalkeeper Kabeya Ntumba.
Denis Iguma's earlier shot had also been saved by the Don Bosco goalkeeper as SC Victoria University intensified their search for goals. Christopher Semakweri and Pembele Mukamisa also missed scoring opportunities for CS Don Bosco.
Morley Byekwaso, SC Victoria University's Coach told Xinhua after the match watched by a small crowd that although his team had bowed out, they had managed to get a win at home.
Byekwaso said since it was the first time to play in continental football for his youthful side, he is happy they have gained some exposure.
"We shall continue to work hard and win more trophies on the local scene so that we can go back and play in CAF competitions," he said.