The 22-year-old - whose Liverpool team-mate Jordan Henderson also misses the trip to Kosovo with a viral infection - featured in the headlines earlier in the week after City striker Raheem Sterling confronted him at England's training centre on Monday, the day after Liverpool's 3-1 victory over City.
Gomez was booed when he came on as a substitute in the 7-0 mauling of Montenegro, while Henderson missed it due to a one-match ban.
Victory assured England of a place at the finals.
"Jordan Henderson and Joe Gomez will miss England's final UEFA EURO 2020 qualifier in Kosovo on Sunday," read a statement from the Football Association (FA) already on Friday.