Pardew accepted a Football Association charge of improper conduct on Thursday following the incident in Newcastle's 4-1 win over Hull City at the KC Stadium last Saturday.
Newcastle fined Pardew £100,000 and issued a formal warning over his future behaviour, while the 52-year-old requested a personal hearing with the FA.
However, Mourinho described Pardew as a "great guy" and gave him credit for accepting responsibility for his "mistake".
"I spoke with Alan a couple of hours after and he knows he made a mistake and he knows he has to pay for the mistake," the Portuguese said.
"For me, more important is that he is a good friend and a great guy. I prefer to stay with a good friend that made a mistake."
After the incident, the League Managers Association's chief executive Richard Bevan confirmed that there was a review being held into technical areas and issues surrounding their use.
However, Mourinho, who was handed a two-match ban for poking Tito Vilanova in the eye during a fixture between Real Madrid and Barcelona, said the problem was not with technical areas but human error.
"I never had a problem to share a small space with other managers," he added.
"I don't think that's a problem. I think the problem is human nature, which is open to mistakes.
"I paid for the mistake, I was suspended for the mistake. Every one of us can make mistakes.
"Alan made a mistake we are not used to seeing. When I had the situations in the dugout, the biggest punishment is not the money, not the matches, but you - to recognise yourself that you made a mistake.
"I think he has a big punishment, with all these things together."
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