Fernando Torres' opener in Amsterdam was cancelled out by an Oscar Cardozo penalty but Branislav Ivanovic struck deep into injury-time to spark Chelsea's celebrations.
Benitez was delighted with the way his players bounced back after admitting they had been outplayed in the opening 45 minutes.
"I think it was a great performance in the second half," he said. "We had some problems in the first half against a very good team, but I am really pleased for the players and everyone involved.
"We didn't have the legs and we had to adjust and push them, but in the end we deserved it because we have worked so hard the whole season."
Benitez was an unpopular appointment halfway through the season and has had a tough job as he always knew he would only be in charge until the end of the campaign, so he is thrilled to have delivered some silverware to the club.
He said: "I am really pleased and really proud because it was not easy. We have been talking about this the whole time.
"If you have to win for people to realise the job we are doing? Well, we won. Hopefully now people will say it is not bad. It depends on the perception.
"But if you analyse everything, we won the Europa League with one striker for every single game. We managed players with yellow cards. Today we only had 18 players.
"If you put everything together you will realise how hard it is. I think we did well. This is a team in transition, with young players.
"You could see the commitment of the players on the pitch. When you have a manager who will leave at the end of the season but they still fight and work hard, you have to be pleased."
Benitez has been credited with getting the best out of Torres, whose opener was his 22nd goal of the season and his 15th since Benitez was appointed interim boss in November.
"We have had a lot of players improving during the season," Benitez said. "Fernando was one of these players. A lot of people said I was appointed to bring the best from Fernando. He has improved a lot so I am really pleased.
"He has working hard with the fitness coaches and medical staff and today he was the difference again."
A great feeling
Chelsea's goalscorers Ivanovic and Torres both savoured their Europa League final win after the match.
"It is a great feeling," Ivanovic told ITV.
"This team deserves this because we have had a very difficult season and a lot of games and today was a hard game, Benfica played well.
"We scored on a set-piece and we work hard on this and the team and the fans deserve this trophy.
"It was great feeling to play in the final and another European one as a final and it is now time to celebrate."
Torres added: "I am very happy, I could not wait and it was a tough game and maybe Benfica deserved more but maybe the individual quality made the difference."
Torres admitted that Chelsea were second best in the opening half.
"The first half was not good enough at all - and we had to change our mentality to win a final and you could see a difference in the second half."