European Champions Inter lost 2-0 to Europa League winners Atletico Madrid after struggling to make an impact on a disappointing night for their Italian fans.
"It was very difficult for our team," Benitez said. "We started well, but we never had the game under control and they were physically stronger and in better condition than us.
"They were better prepared for this game and we have not had enough time to practise together because of the World Cup finals and having so many players back late.
"To have the World Cup and then two international match breaks like this at the start of the season is not good for my preparation. I want to make things change my way, but it will take time."
When Italian reporters accused the Spaniard of changing the tactical system and weakening the team, Benitez responded by saying he had played the same way as his predecessor Portuguese Jose Mourinho, now with Real Madrid.
"We have not changed much and in this game we played the same way as we did against Roma, but the difference was that this time the opposition was much better prepared for us."
He said it was too soon for him to be judged on his team's performances.
"We want to go a step further with our performances, but it is too soon. We need more time if we are to do it the way I want to do."
Atletico coach Quique Sanchez Flores said he was delighted with his team's "memorable victory for our family club".
"This brings great joy to our fans and I must say we played very well and deserved to win. I was very satisfied."
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