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Hazard, one of the revelations of Chelsea's season, hurt himself during his side's 2-1 win at Aston Villa in the Premier League on Saturday.
He travelled to Amsterdam with his team-mates on Tuesday, along with club captain John Terry, who is a doubt with an ankle complaint, but Benitez said he would not feature in Wednesday's game.
"Hazard will not be available," Benitez said.
"John, we will try and see how he feels. But we will decide tomorrow."
Were Terry to be declared unavailable, it would be the second time in two seasons that he has been forced to miss a major European final, after he sat out last year's Champions League triumph due to suspension.
The former England captain was not guaranteed to play in any case, however, having lost his place in Benitez's starting XI, but Hazard's absence will be keenly felt.
The 22-year-old has scored 13 goals and laid on 20 assists since signing from Lille last year and was recently voted into the Professional Footballers' Association (PFA) Team of the Year by his peers.
Wednesday's game gives Chelsea an opportunity to end a turbulent season by joining Juventus, Bayern Munich and Ajax as the only teams to have won all three of Europe's top club competitions, including the now-defunct Cup Winners' Cup.
The Europa League was seen as something of an unwelcome consolation prize after Chelsea's Champions League title defence ended in a humiliating group-stage exit, but midfielder Frank Lampard says that is no longer the case.
"You can't have it your own way every year," he said.
"Last year things went our way and we had a good run to the final. We were disappointed to find ourselves in the Europa League this year, but the closer you get to the final, the more you want to win it."
Victory at the Amsterdam Arena will also make Benitez only the second coach after Giovanni Trapattoni to win the competition with two different clubs, after a previous success with Valencia in 2004.
Benitez faced outright opposition from some of Chelsea's fans when he succeeded Roberto Di Matteo in November, but although some ill-feeling remains, he is proud of his achievements at Stamford Bridge.
"It's a final, so I want to win, and if we can do, I'll be really proud because we've worked really hard in difficult circumstances and you have to give real credit to everyone," he said.
"If we win, it'll be easier and people will realise that to be here at this stage of the competition means we have done well.
"Always you can improve, or make more mistakes. It was not an easy situation at the beginning and I think we managed it quite well."
He added: "We have played 68 games now, two games a week for some time. Imagine any team doing that, reaching semi-finals, and now a final.
"Whatever people say, we feel we have done a good job and we think we can do even better."
Benitez also lamented the short-termism creeping into English football, after Roberto Mancini's sacking by Manchester City on Monday brought the number of Premier League managers to have lost their jobs this season to six.
"England is changing a little bit. I see society is going fast and football is going fast," said the Spaniard, who spent six successful years at Liverpool between 2004 and 2010.
"Everyone decides they want to win on the first day, and it's not easy. When I decided to come to England, it was a five-year project and I was asked to work with young players.
"Now you have to win and if you cannot... It's changed a bit, and I think that it's a pity."
