The midfielder was passed fit for the home game with Newcastle after picking up a knock on international duty.
He had made a lively start to the game, operating towards the left but not tight to the wing.
But he was down in pain, with hands on his face, in the first half.
Although he tried to continue, he was clearly struggling and left the field a few minutes later.
Max De Cuyper went on as sub for the third successive match with Ferdi Kadioglu, who had started at left-back, moving further forward.
Gomez looked bitterly disappointed as he left the field.
Fabian Hurzeler had a few words for him as he headed to the changing room.
Gomez was reported by different Paraguayan sources to have either an injury or discomfort in his thigh in the South Korea game.
He had previously played and scored in a 2-2 draw with Japan in Osaka as Paraguay made an exhausting journey to the Far East as part of their preparations for next summer’s World Cup.
Asked whether he had aggravated the same injury, Hurzeler said: “I don’t think it is the same.
“I think it’s a hit on his hip so I can’t give any more information.
“We have to wait for the scan.”