Liverpool are now languishing third in their Champions League group on three points, three behind second-placed Fiorentina and six adrift of Lyon, with three games to go.
Their Premier League prospects do not look any brighter after four defeats ahead of the visit by reigning champions United.
And, with right-back Glen Johnson joining key duo Fernando Torres and Gerrard as an injury concern, Benitez is under huge pressure to revive Liverpool's season.
Johnson was a late withdrawal before the Lyon defeat and was replaced by youngster Martin Kelly, who himself went off injured late in the game.
"We have to push players now, to keep working and to maintain our confidence," said Benitez.
"We just had too many problems before and during the game. Losing Glen Johnson before the match, and then Gerrard and Kelly during the match, was just too much to contend with.
"It was a difficult game with all our problems, and we had done well to be leading at the break. Then we had two or three chances soon after the interval.
"Had we scored, it would have changed everything."
The Spaniard also insisted he had not risked Gerrard unnecessarily to help the side's predicament.
"It was not a gamble to play Gerrard. He wanted to play and had trained normally for two games," added Liverpool's Spanish manager.
"He was given the all-clear by the doctor, and what happened was just bad luck. He felt something wrong in his groin, and it was wise to come off."
Liverpool will have to win when they come to Lyon in a fortnight - that will be a very hard game for us
Lyon manager Claude Puel
Some boos rang around Anfield when Benitez replaced Benayoun with Andriy Voronin, but the Reds boss defended the switch: "The fans know Yossi is a good player, but I felt he was getting a little tired and I wanted to use some fresh legs.
"We needed to change something, to put a fresher man on - and it was a chance worth taking."
Lyon had their own injury setback when Brazilian centre-back Cris was stretchered off with concussion shortly after Liverpool had taken the lead.
"Cris has had scans on his head. He was unconscious, but he has improved," said Lyon coach Claude Puel.
"Despite that problem, it was an excellent performance. It was a tough match, decided by fine details.
"They put us under a lot of pressure with crosses and high balls into the box, and they took the lead. But we kept our organisation and our shape, and slowly maintained more possession.
"We were the better side in the second period - and we deserved the win.
"But I do not believe we have already qualified. Liverpool will have to win when they come to Lyon in a fortnight - that will be a very hard game for us, because Liverpool will be going for it and attacking."
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