Benitez, whose position at the club has been under threat because of his dispute with the club's American owners over transfer policy, insisted that he had "no personal problem" with either Tom Hicks or George Gillett.
It has been clear in an amazing week at Anfield that the co-owners were furious with Benitez for his insubordination and if Liverpool had gone out of the Champions League against the Portuguese side there was speculation that the Spanish manager would be sacked.
But after seeing two-goal Fernando Torres, Steven Gerrard and Peter Crouch score the goals that keeps Liverpool's Champions League dreams alive, Benitez insisted that he had no problem with the owners of the club.
He said: "Firstly I must thank the Liverpool fans, they are always magnificent."
Supporters staged a protest march to the stadium in support of the manager, and his name was chanted constantly by a packed stadium.
He said: "I knew what was going on, but I was focused on my team and the game. I promise you, I was only thinking of the game and my responsibilities. But thank you supporters, you were fantastic."
But then Benitez dropped his guard on a situation that has seen him remain silent since the weekend when he said: "I do not have any personal problem with the owners, I was just talking about the club's future.
"People have said it was all because of my ego, but that is not the case. I was just surprised a little bit with what has happened.
"I was only trying to improve my club. We will have to wait but it is a strange situation. But I repeat, I have no problems with the owners."
Benitez made a point of shaking every player's hand at the end on the pitch and then turning to applaud the Kop as he left the pitch last.
He said: "It is nothing to do with my ego, it is my responsibility to want to improve my team and my squad.
"I could just do nothing and take my wages at the end of the month. But I need to be involved, and I hope they (the owners) will understand.
"We will talk again, and it is nothing to do with this result putting me in a stronger position, that is not of consequence. I just have ideas for the future, I am in the same situation with the same views that I had before."
Liverpool's players and fans showed their support. The fans chanted "Rafa's going nowhere" at the end, but Benitez said: "I can only thank them for their support firstly for the team, and what they did for me beforehand."