The Brazilian attacker was withdrawn in the 58th minute in south London despite the Toffees trailing in a game they would eventually lose 3-1.
Benitez’s decision was greeted with boos by the travelling supporters but the 61-year-old defended the substitution.
He said: “I cannot explain everything all the time. We have Allan not coming because he has a small injury but Richarlison at half-time we knew, because we could see him limping, he has a problem with his calf.
“We tried to make the substitution at half-time, he said he wanted to try for the second half.
“It was obvious he was not at the level we were expecting and without (Dominic) Calvert-Lewin available, we didn’t want to take the risk.
“We made the substitution but you cannot explain to every single fan why.
“The player was not helping but he knew because he told us and we could see he was not fully fit.
“It was just trying to protect the player and it seems it goes against you, but OK now you have the explanation.
“Hopefully everyone will understand we try the best for the team and the best for the team was to keep our player protected and to make sure we had a player fully fit on the pitch.”
Richarlison’s replacement Salomon Rondon made a positive impression during his 32-minute cameo in the capital.
The summer signing grabbed his first goal for Everton in his 12th appearance and held the ball up well, but the Toffees continue to miss Calvert-Lewin.
England forward Calvert-Lewin has been absent since August with a thigh injury and is unlikely to feature before Christmas.
Benitez added: “He is getting closer. When I say that it is normal but after two injuries we don’t want to take the risk and to lose him for the rest of the season.
“I will say in a couple of weeks he will be fine and then we have to decide with him how he feels.
“I was watching him training the last two or three days and he is getting fitter, much better and stronger.”
A brace from Conor Gallagher and James Tomkins’ second-half goal consigned Everton to a seventh loss from their last nine games.
The result helped Palace end their own poor form of four matches without a win and the Chelsea loanee was delighted.
Gallagher told Sky Sports: “This game was massive for us. We have lost the last three so to get the three points was important.
“I feel we’ve been unlucky in the last few games. We wanted to give the fans a good performance and we did.
“I love it here. Hearing them sing my name is a great feeling and gives me confidence which is amazing for a player.
“Hopefully I can continue to impress them. I always give my all and I try to affect the game as much as I can.”