The Blues became the first defending champions not to make it out of the group stages of Europe's elite competition after Shakhtar Donetsk's 1-0 defeat to Juventus saw the Italian side advance as Group E winners.
The Ukrainians will also be in the draw for the knockout phase by virtue of their better head-to-head record against the west Londoners.
Benitez said the atmosphere in the Stamford Bridge dressing room was hollow but he at least witnessed his first win since taking charge of Chelsea while Fernando Torres scored twice to end a six-game goal drought.
"I think always when you win it is a positive. When it is at home it is even better," said the Spaniard. "The way we won, we had 32 attempts and 18 on target, is really good.
"When you win you have to be happy but at same time we are disappointed as we didn't progress. At least we showed the level and quality we asked for.
"We now have to think about Sunderland (on Saturday) and the Europa League.
"But the game was so good today and we can see a lot of positives for the future. We pressed well, we created chances and scored a lot of goals.
"If you ask ask about Fernando also he scored goals. He has to score. He was playing well and the team was helping him. If we create chances he will score goals."
One game at a time
Chelsea's embarrassing display overall in Europe compounds the poor domestic form that has seen them go seven league games without a win, although Benitez believes Wednesday night's win can kick-start their campaign.
"I'm sure that, playing at this level, we can do whatever we want, but we have to start that in the next game," he said, looking ahead to the trip to Sunderland.
"My idea is one game at a time, but if you remember the four games we've already played there was only 45 minutes we did not play at the right level.
"Manchester City was a difficult game but we performed more or less against one of, if not the, best teams in the Premier League.
"Against Fulham we could have won and had a lot of chances, too. The first half against West Ham was good so everything I am seeing from the players is good, is positive.
"They are progressing, they are improving and they are adjusting to my ideas - the little things we are trying to change - so I think I have to be pleased."
As well as the overall team performance, which included goals from David Luiz - who opened the scoring from the spot - Gary Cahill, Juan Mata and Oscar, Benitez was buoyed by Torres' showing.
"I hope [it is a springboard for him]," Benitez said. "He's shown his desire and quality at the same time.
"If we can play at this level, then I think he can score more goals."
His goals, though, were not enough to prevent Chelsea dropping into the Europa League - a competition many see as an unwanted distraction.
"The Europa League is not important if you don't win," Benitez said. "When you are in the semi-final or the final, everyone wants to win it.
"We know that it is an important competition and we want to go as far as we can and if we can win the competition, we will try to do that."
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