Zanaco defeated the Rwanda champions 1-0 thanks to a 17th minute goal from defender Taonga Bwembya.
It was a dream debut goal from Bwembya who has just joined Zanaco this season from Mufulira Wanderers.
The result sees Zanaco advance 1-0 on aggregate after overcoming the pressure of a 0-0 first leg result at home in Lusaka on February 11.
However, APR continue to stumble on the first hurdle dating back 2005 when they eliminated Green Buffaloes to reach the CAF Confederation Cup pre-group stage.
Zanaco will now will face George Lwandamina’s Young Africans Of Tanzania away in a first round, first leg match on March 11.
Young African advanced to the first round after a 6-2 aggregate win over Ngaya of Comoros.
Ngaya held Young Africans to a 1-1 away draw in the final leg match earlier in the day on Saturday in Dar-es-Salaam.