Mourinho joined Los Blancos in 2010 after an impressive spell with Inter Milan and enjoyed some fierce battles with Pep Guardiola and Barcelona.
El Clasicos during that period were not short of action both on the pitch and the sideline, most notably Mourinho poking Guardiola's former assistant Tito Vilanova in the eye.
Pique has now revealed the extent of Mourinho's impact on the Spanish players in the Los Blancos squad.
"Since he arrived, he knew that on the pitch they were weaker than us," Pique told the Overlap podcast.
"We had a better team for sure, and even the relationships between players.
"I remember going to the national team and after those games it was tough because Mourinho goes to the mind of the player and he says: 'These guys hate you', then you believe that.
"I was in the dressing room of the national team and went to Iker Casillas: 'Hey Iker', and the guy did not talk to me.
"At that time I did not know, but it was the coach he really knows how to go into the mind."