Ligat Ha'Al champions Hapoel were edged out 2-1 at home by Romanian side FCSB in a game where all the goals came in the final 15 minutes.
Hapoel were denied by the reflexes of FCSB goalkeeper Florin Niță, who made smart stops either side of half-time.
Two sharp finishes from super-sub Harlem Gnohéré in the space of five second-half minutes put the visitors in charge.
Isaac Cuenta, another substitute, gave Hapoel a late lifeline with a close-range finish but FCSB held on.
Hapoel may have had more chances and possession on the night but they find themselves bottom of Group G on goal difference, level on three points with FC Lugano and FC Viktoria Plzen.
So qualification hopes hang in the balance, with trips Bucharest and Switzerland to follow before they conclude the group phase against Plzen at the Turner Stadium.
Maccabi Tel Aviv were brushed aside 4-0 by Astana in Group A. A first-half double from Patrick Twumasi plus two more from Junior Kabananga in the second half saw a sharper Astana team run out worthy winners.
Maccabi remain bottom of the group with no wins in three matches. They host Astana on November 2.