He will now return to Arsenal for further assessment ahead of their Premier League clash with Bournemouth next weekend.
Liverpool midfielder Curtis Jones is also out of the trip as he has a personal matter to deal with.
Jones was a late addition to the England squad ahead of the Greece game but was an unused substitute.
Harry Kane was one of 22 players who trained on Saturday, increasing hopes that the captain will be fit after missing Thursday’s game.
Kane could not overcome a knock picked up playing for Bayern Munich in time to feature and his absence prompted interim boss Lee Carsley to deploy an eyebrow-raising formation which had Jude Bellingham playing a ‘false 9’ in front of Phil Foden, Saka, Cole Palmer and Anthony Gordon.
When asked how the defeat might affect Carsley’s future, England goalkeeper Jordan Pickford said: “I’m not the hierarchy.
“It’s never nice for a player or staff to get beat at Wembley.
“We want to win every game we play when we put this shirt on and we didn’t.
“So we’ve got to keep going, dust ourselves down. What can we do better, what can we learn from and move on and get the result on Sunday?
“You’ve always got to learn. You’re never going to be perfect, even when you’re winning games. You can learn a lot from this.
“It’s about recovering well and getting ready for Sunday.”
Defeat leaves England under pressure in Group B2 as Greece opened up a three-point lead at the top.
They must now win their remaining three games, starting with Finland on Sunday before the return trip to Athens and a Wembley fixture against the Republic in the November fixtures.
Pickford hopes skipper Kane will be available after he missed the Greece game with a knock.
“He’s not the record goalscorer for England and has 100 caps for nothing, he leads by example,” he said.
“I think Harry will be fit to go on Sunday.
“Now we’ve just got to go and win away on Sunday against Finland and then the next camp in Greece away and Ireland at home.”
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