The former Madrid midfielder was let go after a 3-2 loss to Barcelona in the Spanish Super Cup final.
Despite Alonso's celebrated success with Bayer Leverkusen, his time at the helm of Madrid was hampered by a gruelling schedule and a squad suffering from physical fatigue.
Following his departure, the club appointed interim coach Alvaro Arbeloa, who is also facing a period of instability.
Perez defends Alonso’s appointment
Appearing on the popular Spanish program 'El Chiringuito de Jugones' for a 40-minute segment, Perez addressed several key issues, including the mid-season dismissal of Alonso.
Perez insisted that appointing Alonso was the right move, attributing the subsequent struggles to external factors rather than poor judgement.
"No, it was not a mistake. It was a matter of circumstances," Perez told host Josep Pedrerol. "It all stems from the Club World Cup; we didn't have a pre-season.
“When you don't have a preseason, you suffer physically. We thought the change would help, but it only worked for a bit before they fell apart again."
Madrid finished behind rivals Barcelona in the La Liga title race and were eliminated from the Champions League in the quarter-finals by Bayern Munich.
With presidential elections on the horizon, the club's leadership must now decide whether to appoint a permanent manager or stick with Arbeloa, all while managing the long-term future of key players like Vinicius.