Durban City carried a narrow advantage into the second leg in Burundi, having won 1-0 at Moses Mabhida Stadium the previous week. They quickly removed any uncertainty, with Kyle Jurgens heading in John Mokone’s cross inside the opening minute.
Rukinzo responded with sustained pressure, but City’s defence held firm through much of the first half. The visitors then strengthened their position in the tie when Samkelo Maseko scored his first goal in the competition in the 35th minute.
That left Durban City 3-0 ahead on aggregate and allowed head coach Khalil Ben Youssef to manage the final stages. Ethan Brooks, Makua and Mthembu were introduced just after the hour mark, replacing Tyler Sanger, Jurgens and Bandile Shandu.
Rukinzo pulled a goal back with seven minutes remaining, but the late effort failed to unsettle the South African side, who held on for a 2-1 victory on the night.
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The result sends Durban City through alongside Kaizer Chiefs, who have also reached the next stage of the competition.
City will now face AS Port-Louis 2000 of Mauritius, who advanced after overcoming Jwaneng Galaxy. The tie offers Ben Youssef’s side another opportunity to build on their domestic cup success and establish themselves in continental competition.