Andriy Voronin was the culprit of the most glaring miss, while Fernando Torres, who was nursing a hernia problem, and Lucas Leiva also failed to turn Liverpool's superiority into goals.
It seemed like Babel had grabbed a winner with his late strike but the defensive vulnerability which has dogged Liverpool's season so far struck at the worst possible time to let Lisandro in and break the visitors' hearts.
Liverpool were already battling for Champions League survival going into the game and the Anfield club's manager Rafael Benitez had wanted his side to show confidence, character and belief.
He had also drawn on the club's anthem of You'll Never Walk Alone, as well as a record which has seen the Reds win on their last four visits to France to try to motivate his players.
And the Liverpool players gradually started to show the qualities demanded of them after a tentative start.
Torres had their first chance but he sidefooted straight at Lyon keeper Hugo Lloris from 12 yards after a low Emiliano Insua cross was deflected into his path.
Another Insua cross came off Yossi Benayoun for Dirk Kuyt and he steered a shot which would have dipped under the Lyon crossbar but for Lloris to again rescue his side by tipping the ball over.
Liverpool's control of the game grew as the tie progressed and they should have converted it into a goal when Voronin was presented with a glorious chance.
Javier Mascherano's quick-thinking and vision saw him release the Ukrainian clean through on goal with a long free-kick over the top but Voronin shot straight at Lloris.
And, while the profligacy would have frustrated Benitez, the signs were encouraging from a Liverpool side with an air of the walking wounded about them because of a severe injury crisis.
However, Lyon also had their problems with right-back Anthony Reveillere and midfielder Miralem Pjanic having to go off injured as the home side struggled to make an impact.
Liverpool and Lucas should have taken advantage but Lloris brilliantly saved to his left as the Brazilian tried to curl as shot around him.
The ball was cleared off the line from Kuyt's overhead kick from the follow-up as the urgency of the visitors' situation saw them push forward in greater numbers.
Reina crucially produced a save from Lisandro after confusion between Sotirios Kyrgiakos and Daniel Agger to keep Liverpool in it before Babel's stunning intervention.
The Reds had to hold on for about 10 minutes but failed to do so and now face failing to progress from the initial group stage for the first time since 2002/2003.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.