The Ugandan Cubs, 4-0 winners in the first leg two weeks ago in Kampala marched on 7-2 on aggregate.
The visitors were two goals up at half time with strikes from Charles Ssebutinde and Julius Poloto. However, the lead was canceled by the Rwandans after recess through Rachid Bigiraneza who scored a brace.
But it was Uganda who laughed last after Shaban Muhammed scored the match winner on 74 minutes to complete a famous double against their East African counterparts, who finished the game with 10-men after captain Djabel Manishimwe was sent off four minutes from time.
The Cubs will face Zambia, 5-0 winners against Botswana in Gaborone also on Friday.
Patson Daka scored twice whilst Pumulo Siwanga, Garry Mwelwa and Enock Mwepu scored once each to silence their hosts and advance 6-0 on aggregate.
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