The former Bayern Munich and Inter Milan star was hauled off after just an hour despite becoming the club’s record signing last summer.
Hughes’ decision to sub the Switzerland international during Saturday’s game at St Mary’s was seen by some as a warning - but the Stoke manager has explained that it was purely down to Shaqiri picking up a slight hamstring injury.
Hughes told the club’s official website: "He had a little tightness in his hamstring to be fair, and that was the reasoning behind taking him off when we did.
"He wanted to go out and play the second half but it was important that we protected him a little bit, which is what we did.
"I was really pleased with what he offered us once more today. You can see each game he plays that he is adapting and showing the undoubted qualities he possesses."
Stoke have been in good form this season, winning four of their last six domestic matches while also failing to concede a goal away from home for over seven hours.
The Potters, 11th in the table, travel to the Stadium of Light this weekend to face Sam Allardyce’s Sunderland and club captain Ryan Shawcross is hoping that the club can build on their current league position.
He said: "We’re beginning to look more fluent in our performances, we have some very talented players so hopefully we can continue this good run of form.
"Clean sheets are what we strive for. It’s never easy, it’s a tough league and teams are always going to create chances.
"There are other players who are fighting to take our place so we aren’t resting on our laurels, we’ll carry on working hard and hopefully get some more clean sheets."