Saka was substituted in the first half in the 2-1 loss at Wembley having been seen clutching and testing his right leg.
The 23-year-old winger's withdrawal means he will not feature in England's fourth Group B2 match against Finland on Sunday.
"He's been assessed but in the build-up to the first goal you could see he'd felt something in his leg," interim manager Lee Carsley said after the match.
Liverpool midfielder Curtis Jones has also left the camp and will too miss the trip to Helsinki due to a personal commitment.
Jones was a late addition to the squad and was an unused substitute against Greece earlier in the week.
Meanwhile, there was a boost for Carsley with captain Harry Kane and Jack Grealish taking part in training on Saturday.
The pair missed the Greece match through injury with Kane unable to shake off a knock to his ankle.
