Hicham Fatini put the North Africans ahead on 10 minutes in the Moroccan capital and Adil Meskini added a second goal entering the closing stages of the second round, first leg qualifier.
It was a predictable result given the growing stature of FUS, who created one of the biggest shocks in African club football history by winning the second-tier competition last year, and the inexperience of Kunda.
Having won the domestic cup as a second division side, Kunda gained promotion to the elite league but their only international experience was sinking Ports Authority of Sierra Leone in the previous round.
FUS began an epic 18-match journey to glory last year in Senegal and they should survive the return match there to book a third-round tie against Primeiro Agosto of Angola or AC Leopards of Congo.
Primeiro appear to have the edge in that tie after building a 2-0 lead in Luanda thanks to goals from 'Roger' and 'Bena' although the Congolese did not help their cause when a player was red carded.
It was a mixed weekend for Moroccan challengers with Moghreb Fes surprisingly held 0-0 at home by Sahel of Niger, a central African country working hard to rid itself of a 'whipping boys' football tag.
Compatriots ASFAN mocked the form book to reach the 2010 Confederation Cup mini-league phase and Sahel are well placed to reach the last-16 stage in Niamey next month.
Watching the Nigeriens is not for goal lovers, though, as this was their third consecutive 0-0 draw in the competition and they owe a place in the second round to a penalty shootout victory over Togolese team Dynamic.
Ugandan club Victors could not live up to their name as they conceded a late goal and had to settle for a 1-1 home draw with 1994 African Cup Winners Cup title holders DC Motema Pembe from the Democratic Republic of Congo.
Yuda Mugalu converted a Henry Kalanzi cross on 19 minutes for the local team in a tie delayed 24 hours by torrential rain in Ugandan capital Kampala and Ilongo Ngasanya equalised.
The stalemate left rival coaches George Nsimbe and Adede Moko confident that they will make the next round and a probable pairing with Egyptian coast guard club Harras al-Hodoud.
Victors Nsimbe said his team "play better away from home" while Moko, coach of the 1994 trophy-winning side, countered that "the artificial turf in Kinshasa will help us as we struggled on a muddy pitch".