State unit spokesman Sachin Sawant met state Election Commissioner J S Saharia and lodged the complaint, a day after Saharia said they will look into the matter only after receipt of the plaint.
The advertisement, featuring Khan, appeals to Mumbaikars to vote for transparency and good governance.
"Despite the EC guidelines banning ads in the print and electronic media after the campaign ends 48 hours before voting, the organisation 'Mumbai First' issued the advertisement in prominent newspapers on the voting day yesterday to help the BJP," Sawant said.
The advertisement, which has appeared in English, Marathi and Hindi dailies, prominently uses words like 'transparency', 'change', 'pardarshita' and 'parivartan'.
More From This Section
These words were used by a party during poll campaign. 'Transparency' was the ruling BJP's main poll plank.
Sawant claimed Chief Minister Devendra Fadnavis headed one of the committees of the organisation.
"This is a clear violation of the model code of conduct. Finding loopholes in law and side-stepping rules and regulations is a criminal mindset. A criminal offence should be filed against the BJP, Mumbai First and Aamir Khan since his photograph is used in all the ads," Sawant said.