Substitute Kaka had just sealed victory at the Bernabeu with an 82nd-minute strike when Mourinho left his technical area to pass in front of the visitors' bench and punch his arm in the air while facing the stands.
Villarreal substitute Cani reacted by lobbing a water bottle at him and, although it did not hit the Portuguese, was shown a red card by referee David Fernandez Borbalan.
"I went to celebrate the goal with my son who was behind the visitors' bench, and the Villarreal players thought I was provoking them," Mourinho told the post-match news conference.
"I hope that when one swears on their son they believe you. I think this (situation) comes from a state of affairs where everything I do is always classed as negative."
Villarreal coach Juan Carlos Garrido, who was highly critical of the referee saying he was scared to blow against the home side, did not take the matter any further.
"I think Mourinho went to celebrate with the fans and my players took a different interpretation, and the referee sent off Cani," Garrido told reporters.
Mourinho has often been accused of provoking opponents on and off the pitch, and famously had a run in with Barcelona goalkeeper Victor Valdes after his former club Inter Milan knocked Barca out of the Champions League semi-finals last season.
After the final whistle Mourinho sprinted across the Nou Camp pitch celebrating, to howls of protest from the Barca fans. Mourinho said he had simply gone to enjoy the moment with the Inter fans who were in the upper tiers on the far side of the ground.
