The petition was filed on behalf of Ashok Soni and Abhishek Bhargava in the court of additional sessions judge Justice Jitendra Singh Kushwaha.
Accepting the petition, the court fixed December 3 for hearing.
The plea said Aamir Khan was a "role model" for the youth of the country, and he had a huge fan following, and thus his comment on growing intolerance will vitiate the atmosphere in the country.
The petitioners said the creation of such a situation was a criminal offence.