The Liverpool defended was booed at Wembley in the 7-0 rout of Montenegro after his altercation with Raheem Sterling earlier in the week.
But Gareth Southgate will now be without Gomez after he picked up a knock in training on Friday, while club teammate Jordan Henderson has not recovered from a viral infection and also drops out.
An England statement read: “Jordan Henderson and Joe Gomez will miss England’s final Uefa Euro 2020 qualifier in Kosovo on Sunday.
“Henderson arrived in camp with a viral infection that has not fully cleared. Meanwhile, his Liverpool team-mate Gomez sustained a knock in training on Friday and has not recovered sufficiently enough to travel.
“The pair now return to their club meaning the Three Lions will head to Pristina on Saturday with a 23-man squad.”
The pair will now be a doubt for the Reds's Premier League match against Crystal Palace on Saturday, November 23.
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