Despite setting up Mohamed Salah's winner against Huddersfield Town before impressing against Red Star Belgrade in the Champions League, Shaqiri had to settle for a place on the bench for Saturday's Premier League clash at Anfield, with Adam Lallana preferred from the start.
And Klopp has emphasised that Shaqiri was rested, rather than dropped, with Liverpool unsure of how the 27-year-old would react to a congested fixture list.
"Shaq came in and was involved in two nice goals, which is always good," Klopp told a news conference.
"That made it so hard to leave him out because he was a good player for that game, but we had to think about if it was the right thing to do.
"He played four games nearly 90 minutes in a row. Both international games for Switzerland, then Huddersfield and Belgrade for us.
"It was clear, we don't know Shaq long enough to know how he reacts. Sometimes you have to protect players until you know them a bit better.
"I thought the line-up we chose was good, it was good for Adam to start, he was really involved especially in the first half, less in the second which is completely normal.
"We decided differently, but football games are 97-98 minutes and you need 14 players for that. We only used 13 but bringing on that quality is a massive difference."
26 - Liverpool have won 26 points in their opening 10 Premier League games this season (W8 D2 L0) - their joint-best start to a Premier League season after 10 games (also 26 in 2008-09). Threat. pic.twitter.com/4NsID1O9PA— OptaJoe (@OptaJoe) October 27, 2018
"Everybody is happy to have Shaqiri here. He is a top man and as a player he is fantastic," Mane told Liverpool's official website.
"He is a great player; he has come and looked like he has been here for years. He's going to help us score more and give assists."