Francis Gillot's side have won only one of their first eight games in Ligue 1 to sit just one place above the relegation zone and this was their second successive European defeat to leave them bottom of Group F.
Jussie's goal early in the second half raised hopes of a rare win but Barach Yitzhaki and substitute Dor Micha turned the game around for Maccabi, who have four points after drawing with APOEL last time out.
Maccabi's Eran Zahavi saw an early shot tipped over before Yitzhaki shot wide.
At the other end, Diego Rolan sent one effort wide before testing goalkeeper Juan Pablo with another following a good counter-attack.
Hadi Sacko then had shots blocked by Carlos Garcia and Eitan Tibi in the same attack and Rolan's excellent free-kick was repelled by Juan Pablo.
Zahavi went close again while for Bordeaux, Rolan headed Jussie's cross just over and Sacko scuffed wide when set up by Nicolas Maurice-Belay.
Maxime Poundje's misdirected cross threatened the visitors' goal before the interval.
Bordeaux took the lead three minutes after half-time when Maurice-Belay and Obraniak created the opportunity and Rolan crossed for Jussie to head home.
Tibi forced a scrambling save from Kevin Olimpa before Bordeaux lost Maurice-Belay to injury, in an incident which also saw the full-back bizarrely booked for his protests as he lay prone on the turf following Gal Alberman's wild challenge.
Further controversy surrounded Maccabi's equaliser with 20 minutes remaining. Rade Prica crossed from the left to an unmarked Yitzhaki, who tapped in with Bordeaux clamouring for an offside flag.
Prica had a shot blocked by Poundje and was again involved as Maccabi took the lead in the 79th minute, although Micha both started and finished the left-wing counter-attack.
Olimpa saved well from Yitzhaki to save a tired-looking Bordeaux from further damage but their frustration told in stoppage time when Ludovic Obraniak fouled Omri Ben Haroush and was booked, along with Ludovic Sane, for dissent.