The Reds will travel to the Serbian capital of Belgrade to take on Red Star in their fourth match of Group C on Tuesday evening, but Shaqiri has been left out in an effort to avoid promoting a "political message" due to his Albanian heritage.
Jurgen Klopp's side now sit top of Group C and go into the Belgrade clash as heavy favourites having comfortably dispatched Red Star at Anfield recently.
Kosovo-born Shaqiri was a notable absentee from the squad travelling to Serbia yesterday - with Klopp seeking to avoid unnecessary distractions.
Nigeria have lift-off in their World Cup, while Switzerland and Brazil leave it late.
Shaqiri made headlines during the 2018 World Cup in Russian Federation after celebrating his victor for Switzerland against Serbia by crossing his hands to imitate an eagle, which appears on Albania's flag.
"This is a big event for Red Star, for Belgrade, for Serbia, and the whole region", he said in his pre-match press conference.
"I said it after the first game, I really saw it in that game".
"We have to make sure that we remain focused on football".
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"Paris is not an easy place to go to and then we are at home to Napoli but tomorrow is not our only chance".
In an effort to avoid controversy and unnecessary "distraction" Klopp has now made a decision to leave Shaqiri at home, stating his intentions to be "respectful" and to exclusively focus on the football.
"My job and your job as well is not to do questions which provoke a kind of answer", Klopp said.
"It was a hard situation if you want, usually you don't think about things like that before a game but we had to think about it".
"We are in Serbia and we respect that 100 per cent". That's how the world is. Politics always has always influence on life, on the life I live at least, and that's how it is.
"But we are not here for that, we are here to play football. That's what we want to do and that is why I made that decision".
Asked about the toughest away atmosphere he has experienced as a manager in Europe, Klopp told journalists: "I think it was Sevilla. This is a proud football club and they want to strike back".