Lisandro Lopez's late equaliser denied Liverpool a crucial victory as Lyon secured Champions League progression with a 1-1 draw in France.
Substitute Ryan Babel came off the bench to smash a superb opener for Rafael Benitez's side but Lisandro poked home in the dying seconds to seal a top-two berth in Group E, leaving Liverpool with a mountain to climb to reach the last 16.
The Merseysiders are now five points behind Fiorentina with only two games to play; at home to the Serie A side and away at Debrecen.
Fernando Torres was deemed fit enough to start and despite looking far from 100 percent, the first chance fell to the Spanish hitman, who weakly side-footed Emiliano Insua's low cross straight at the feet of Hugo Lloris with 12 minutes on the clock.
Another Insua delivery caused more problems in the hosts' defence five minutes later, and again Lloris was forced into a save, having to tip over Dirk Kuyt's dinked effort as the visitors carried the fight to the Frenchmen on their first ever trip to the Stade Gerland.
Lloris was being kept a busy man, but the French keeper should have been given no chance when Andriy Voronin got in behind the Lyon defence. The Ukranian's effort was poor however, typical of a striker out of form and lacking in confidence, and Lloris was again able to save with his feet to ensure Claude Puel's men went in level at the break.
Lyon began the second period on the front foot, with Lisandro Lopez and Bafetimbi Gomis both missing the target following two Aly Cissokho crosses but Liverpool soon regrouped and wasted a wonderful opportunity to open the scoring in the 68th minute.
Again it was Lloris who denied the Reds, blocking Lucas' close-range effort, but the keeper needed a hand from Cissokho, who cleared Kuyt's overhead effort from the rebound off the line.
Pepe Reina was forced into his first real save with 18 minutes remaining, the Spanish stopper blocking Lisandro's effort following Sotirios Kyrgiakos's poor back-header and Lyon were made to pay for the profligacy in spectacular fashion with seven minutes remaining.
Substitute Babel picked the ball up 30 yards from goal before advancing a couple of paces and unleashing an unstoppable drive that flew into the top corner with Lloris well beaten.
Babel fired another effort well wide before Lyon grabbed their heart-breaking 89th-minute equaliser.
Kyrgiakos was caught out as Lisandro steadied himself before poking past the advancing Reina, seconds before the 90-minute mark.