Both players have shown good form ahead of the clash at Old Trafford on Sunday.
Benitez said: “For us, Fernando is very important. If he had been fit all season the gap to the top would have been smaller.
“If Fernando is fit he’d score in a lot of games, so it is very simple. It would have been a different season for us if he had been injury-free and played more.
“Would I swap him for Rooney? Not really. Fernando is a fantastic player and there’s no doubt Rooney is very, very good.
“But Fernando is our player, the fans love him and we want to keep him.”