Celta secured all the points in Vigo with a late penalty, but Emery has criticised referee Juan Martinez Munuera's decision to penalise centre-back Federico Fazio for handball.
"It looked clear it was going to be a draw but the referee decided the game," Emery told reporters. "He could have whistled for a foul for Sevilla or a penalty.
"They tell me it's not that clear on television either so it's a shame that the referee was so strict with his decision, but he should have given a foul before the penalty."
Sevilla remain six points off a Champions League position in La Liga.