Shaqiri started against Lincoln City in the previous round and was expected to start against the Gunners on Thursday night.
But it was Harry Wilson who came into the side instead, with Shaqiri not even featuring amongst the substitutes bench.
Shaqiri, who played just 185 minutes in the Premier League last year, is expected to move on this summer should the right suitor appear.
According to reports, talks over a potential exit are advancing with another club. Klopp, when questioned by Sky Sports after the game, hinted a move may now well be close.
"It's the time of the year where some things are happening in the background," Klopp said.
"We have to react sometimes and that's what we did."
A move to Italy has been rumoured for some time, with Shaqiri thought to be keen on a return to Italy following his stint with Inter Milan in 2015.
Despite having some standout performances during his debut season, a combination of injuries and match fitness has seen him fall out of the pecking order.