Reds boss Jurgen Klopp has taken the decision to omit the winger from his 21-man travelling party, which will leave Merseyside for Serbia later on Monday morning.
Klopp is keen to avoid unnecessary distractions as Liverpool look to take a significant step towards qualification from Group C on Tuesday night.
The manager was aware that Shaqiri’s involvement in the game would crank up hostility levels in the Rajko Mitic Stadium. The 27-year-old angered Serbian supporters with his celebration when scoring a last-minute winner for Switzerland at the World Cup back in June.
After scoring in Kaliningrad, Shaqiri placed his hands together to form the double-headed eagle which represents the Albanian flag. The former Stoke City man also wore the flag of Kosovo on his boots.
Shaqiri, who was born in the former Yugoslavian city of Gjilan to Kosovan-Albanian parents, was booed and jeered by the handful of Red Star fans who made it into Anfield for the reverse fixture two weeks ago, and Liverpool are aware that with a sell-out crowd of 50,000 expected in Belgrade, his presence would be risky.
Kosovo declared independence in 2008 but Serbia refuses to recognise it as a state and relations between the two countries have been tense.
Explaining Shaqiri’s omission, Klopp told the club's official website: "It’s a situation where we will go to the fantastic city of Belgrade as a football team to play football.
"We have heard and read the speculation and talk about what kind of reception Shaq would receive and although we have no idea what would happen, we want to go there and be focused 100 per cent on football and not have to think about anything else, that’s all.
"We are Liverpool FC, a big club, a football team but we don’t have any message further than that. We have no political message, absolutely not. We want the focus to be on a great game of football, free from anything else.
"We are keen to be respectful and keen to avoid any distractions that would take focus away from a 90-minute-plus contest that is important for football and only football. So for that reason, Shaq is not involved and he accepts and understands this. Shaq is our player, we love him, and he will play for us a lot of times, but not on Tuesday.
"I have heard so many wonderful things about the city of Belgrade, and the country of Serbia as a whole, from friends and colleagues who’ve visited before, so now I’m really looking forward to taking Liverpool there for a great game of Champions League football."
Klopp has been boosted by the return of Dejan Lovren and Naby Keita, both of whom missed Saturday’s game at Arsenal. Jordan Henderson and Nathaniel Clyne miss out.
"We will take pretty much everyone," Klopp said. "Clyney is ill and will not be involved, but Dejan and Naby are back in the travelling squad.
"Hendo was close, but not close enough. He needs two proper sessions for his fitness, which he will get at Melwood, with Shaqiri and hopefully Clyney if he is back from illness. They both should be fine for the weekend."
Travelling squad: Fabinho, Van Dijk, Wijnaldum, Lovren, Milner, Keita, Firmino, Mane, Salah, Gomez, Alisson, Sturridge, Moreno, Lallana, Mignolet, Robertson, Origi, Solanke, Matip, Kelleher, Alexander-Arnold.