Decorated Spanish defender Pique has struggled for form this season and was not included in the squad for Barcelona's shock La Liga loss at the Camp Nou.
However, Zubizarreta has said that the final decision on team matters falls with Enrique.
"I do not know why [Pique was dropped]. The calls are made by the coach and he chooses the best XI," he told reporters.
Pique has been strongly linked with a move away from the Catalan giants in recent weeks.