"For 75 minutes we played with a lot of quality, we were a perfect team. Scoring four goals against Lyon is not easy, but we surprised them," Benfica coach Jorge Jesus told reporters.
"In my dressing room talk I told the players it would be an easy game. I only got it right until the 75th minute. We ended up being surprised with the three goals we conceded," he added.
Midfielder Carlos Martins created four goals as Benfica survived the late fightback and revived their hopes of reaching the next round.
The combative midfielder's tense free-kick into the crowded Lyon box allowed striker Alan Kardec to tower over the defence to head in for the opening goal on 20 minutes. He then fed Fabio Coentrao for the second after a flowing counter attack.
Martins, who has been on fine form this season and made a return to the Portugal squad, was also involved in the third, his corner to the first post allowed Javi Garcia to head in three minutes before the break.
From another counter attack Martins sent Coentrao through and he scored with a delightful lob in the 67th minute before Yoann Gourcuff and substitutes Bafetimbi Gomis and Dejan Lovren, in the fifth minute of stoppage-time, pulled goals back for the French side.
"The cherry on the cake would have been ending the match winning 4-0, 4-1 or even 4-2, but the result doesn't take away our right to say we played a great game," Jesus said.
Benfica's main creative force, Argentine playmaker Pablo Aimar, was ruled out moments before kick-off with an upset stomach, but his replacement Eduardo Salvio looked dangerous throughout.
He forced Hugo Lloris to block away a left-footed shot from outside the box on 12 minutes and called the keeper into action again in the 39th minute after a fine run on the right wing.
Lyon, missing their regular striker Lisandro Lopez through injury, looking disjointed going forward and rarely threatened until their first goal.
"We got in to the game too late, Benfica's fourth killed any hopes we had," Lyon's Brazilian defender Cris said.
Barring two early disallowed goals from Jimmy Briand, their only clear chance in the first half came on 28 minutes, when the striker's overhead kick from a cross from Anthony Reveillere went wide.
Gourcuff's goal with a crisp shot from near the penalty on 75 minutes, Gomis's tap-in 10 minutes later and Lovren's headed goal deep into injury time came too late for Lyon.
"After the first 15 minutes we gave Benfica the ammunition to punish us. But given the conditions, we did well to fight back," Lyon coach Claude Puel said.
Lyon, however, still lead the standings with nine points followed by Schalke 04 on seven and Benfica on six.
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