Benitez was criticised by Everton fans for taking Richarlison off against Palace but was keen to highlight his injury at full-time.
"Richarlison has a problem with his calf," said the Toffees manager. "We knew and were trying to protect him at half-time.
"He wanted to try to carry on. Without Dominic Calvert-Lewin we cannot take this risk [of Richarlison aggravating his problem].
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"We put a player who was fresh on. He knew, we knew he wasn't fully fit. It wasn't helping with the arms [Richarlison looking annoyed].
"I said we could change him at half-time and nothing would happen. He wasn't doing too much in the second half."
The news is another blow for Benitez, who could be without eight players for Everton's Premier League trip to Stamford Bridge.
Dominic Calvert-Lewin is still recovering from a thigh complaint and so is Tom Davies, who has a knee injury.
Both Allan and Yerry Mina have muscular problems, while Lucas Digne's future remains unclear after reportedly falling out with Benitez.
And captain Seamus Coleman is still being assessed after sustaining bone bruising and soft tissue damage against Crystal Palace on Sunday.
The Toffees are currently 14th in the table - seven points above the relegation zone - and have won just one of their last 10 Premier League outings.
Former Liverpool midfielder Danny Murphy believes Benitez is "doomed" at Everton because of his lack or resources and Anfield links.
"He doesn’t have the squad to pull it round," said Murphy when speaking to talkSPORT. "He can’t take Everton to a level he needs to for the Evertonians to be happy with that squad.
"When he first went in there I thought from a footballing perspective, what he’s done before, it looked like a decent appointment.
"I forgot, not living in the area and not thinking about it, about the Liverpool connection and the things he said about Everton, it was always destined to end in turmoil."
Speaking about Benitez's alleged bust-up with Digne, Murphy added: "Rafa’s got a history of falling out with players who don’t tow the line.
"Xabi Alonso, Fernando Torres, John Terry. At Real Madrid you had [Sergio] Ramos, [Cristiano] Ronaldo. Alonso being the obvious one at Liverpool.
"What he’s done with Digne, he’s cut his nose off to spite his face. Maybe he’s not playing because he’s questioned him.
"But he’s put Ben Godfrey, who’s a centre-back, at left-back. And he can’t play at left-back, [Palace ace] Jordan Ayew destroyed him."