A big win for the Cypriot side in Moldova would have seen them retain their hopes of staying in one of the continental competitions
Super Eagles goalkeeper Francis Uzoho was denied a clean sheet as Omonia Nicosia suffered a 1-0 loss to Moldovan side Sheriff in the Europa League.
Nigerian forward Ibrahim Rasheed got the winning goal for Sheriff in the 87th minute to send Omonia Nicosia out of Europe.
Sheriff, though, finished third behind Real Sociedad and Manchester United and dropped down to the Europa Conference League.
In Group G, Super Eagles winger Moses Simon was influential as two late goals from Mostafa and Blas powered Nantes to a fine 2-0 win at Olympiakos.
And with league leaders, Freiburg holding Qarabag to a 1-1 draw, Nantes slipped into second place to qualify for the next round alongside the Germans.
Exciting Nigerian youngster Victor Boniface was a second-half substitute as Union Saint-Gilloise lost 1-0 to Union Berlin in Belgium.
Helped by three goals and two assists from Boniface, Union SG had earlier booked their place in the quarterfinals as group leaders.
Union Berlin, however, pipped Braga to a playoff spot with the win.