Algeria and Morocco share a nearly 2,000 km (1,242 miles) border, which has been a source of tension since independence from French colonial rule.
The border is currently closed between the countries and Algeria severed diplomatic ties three years ago.
A long-running dispute about Western Sahara, a sparsely-populated territory annexed by Morocco in 1975, has also strained relations.
Its indigenous Sahrawi people, led by the Polisario Front and with a government in exile in Algeria, mounted a 16-year-long insurgency that ended with a UN-brokered truce in 1991.
Against that backdrop, Algerian customs officials seized RS Berkane’s kit on the squad’s arrival in the country last month.
The Moroccan side refused to wear alternative shirts and did not emerge from their dressing room for kick-off in the first leg on 21 April.
Host side USM Alger were punished with a 3-0 defeat by a Caf panel, and an appeal against the decision was rejected by the continent’s governing body.
A Caf committee has previously granted permission for Berkane to wear the shirts with the extended map, and Faf and USM Alger failed in a bid to overturn that in a previous request to Cas on 26 April, two days before the second leg.
USM Alger travelled to Morocco for the return tie but did not take to the field on Sunday, with the match was cancelled and Berkane handed another 3-0 win.
The Algerian club’s hopes of retaining the Confederation Cup title now appear to lie with the case at Cas.