Dembele has been struggling for form since his return from injury over the New Year and was left on the bench for Saturday's win. Fellow subs Philippe Coutinho and Aleix Vidal took to the field instead.
Valverde insisted: "Dembele on the bench? It was a technical decision.
"It was thought that Aleix Vidal could help us with his deployment and his defensive work."
Coutinho's benching also raised eyebrows on the day.