The midfielder said family problems forced him to miss his country's friendly against Paraguay, and the Bayern Munich boss supported his decision to stay with his son.
Bayern Munich coach Josep Guardiola says he supports Arturo Vidal's decision to drop out of the Chile squad last week.
Vidal courted criticism for La Roja in the summer when he was caught drunk driving as he crashed his car during the Copa America, after which he was handed a two-year driving ban.
The midfielder was again center of attention as he pulled out of Jorge Sampaoli's squad to meet Paraguay, insisting family issues were the reason, which Pep has insisted was a valid reason.