Disposing of the matter, Additional Chief Judicial Magistrate S C Godara, Jaipur City, allowed Khan to deposit the fine through his counsel.
Khan, co-owner of Kolkata Knight Riders, was summoned by the court in May on a complaint that he was seen smoking on April 8 during a match between his team and Rajasthan Royals at Sawi Man Singh Stadium.
The actor, who drew flak for smoking in public, had pleaded guilty and expressed his willingness to pay fine before the court which had also allowed him exemption from personal appearance.
The matter came up before the court on a complaint filed by Anand Singh, who runs the Jaipur Cricket Academy, a private club.
He had sought action against Khan under section 5 read with 11 of Rajasthan Prohibition of Smoking Act, 2000, which prohibits smoking at a public places.
Singh filed the complaint on April 9 on the basis of pictures published in newspapers the next day after IPL match in which Khan was seen puffing away in public.
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Anti-tobacco activists have been demanding that government bring in provisions for harsher punishment, including a big fine and imprisonment especially for habitual offenders of anti-tobacco law.
"Such a step would deter habitual offenders like filmstars who usually think they are above law and for whom the nominal fine is not a big deal," Shekhar Salkar, General Secretary of National Organisation for Tobacco Eradication (NOTE), had said.