The Match of the Day pundits assessed the Liverpool manager's decision and claimed the Swiss star has every right to be "fuming".
Shaqiri put in a remarkable performance at Anfield after he was handed his first start for the club since he joined from Stoke this summer.
The Reds were 3-0 up by half-time after Wesley Hoedt scored an own goal before Joel Matip and Mohamed Salah found the net.
Despite assisting Salah's goal with a remarkable free-kick, the 26-year-old was forced to spend the second half on the sidelines.
During the post-match analysis, Gary Lineker said: "We don't often do a positive piece of analysis on a player that gets hooked at half time, but in Shaqiri we will make an exception."
And Jermaine Jenas responded: "I'm not sure he was hooked, he was taken off. If it was me, I'd be fuming after the display he put in during the first half."
But Klopp defended his decision to substitute him and stated that the team were struggling defensively in the first half.
Speaking about the change, he said: "It was not easy to be honest. It's my job to sometimes deliver news that nobody wants to hear.
"That's how it was at half-time but he is a fantastic boy. I explained it to him so it's no problem.
"Usually I don't explain substitutions at half-time, but I thought it made sense. It's just good to have the free-kick was outstanding.
"The whole team was not right used to what we did today. As a new player, usually you struggle most but he didn't – he tried everything.
"The only problem was defensively.
"Offensively, it was a good idea, but, how I said, we have to work on that more often. But he was good and I liked it."
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