In his petition, Rajinikanth said he has "never endorsed" any film or product using his name as it might "mislead his fans".
Justice S. Tamilvanan, before whom the case came up for hearing, issued interim stay on the release of the film with the title and content.
"Rajinikanth's acting, style and distinct personality have contributed to his mass popularity, which he has attained over the years through his larger-than-life appearances, signature dialogue delivery and age-defying stunts in his films," read the petition.
"Rajinikanth's popularity is likely to mislead his fans into believing that 'Main Hoon Rajinikanth' has been approved by him. It is to prevent such hysteria and confusion among public, he has always chosen to stay away from endorsing any film or product," said the petition.
Directed by Faisal Saif, "Main Hoon Rajinikanth" features southern actor Adithya Menon in the lead as a CBI officer-cum-contract killer Rajinikanth Rao.
The film, produced by Varsha Production House, also features Kavita Radheshyam, Smita Gondkar, Reema Lagoo, Sunil Pal, Ganesh Yadav and Shakti Kapoor in important roles.
Rajini also contended that a film based on his "name or image" is a violation of his "privacy" and accused the producer of cashing on his "super hero image".
The Tamil superstar also said that neither the film's producer nor director had approached him seeking "written" or "oral" permission to use his name in the film.