The accused, who was identified as Kamaluddin alias Kamaal, a resident of 24 Parganas district of West Bengal, was immediately nabbed by Bukhari's Personal Security Officers (PSOs) and later handed over to local police.
An FIR under section 307 (attempt to murder) was filed at a local station.
"The incident took place around 6 pm when the Imam was leading the namaz of 'Maghrib'.
Man, said to be 'mentally unstable', suddenly threw a plastic bottle which had kerosene, at him from behind. The attacker was caught by Imam's PSOs. He has been taken to the nearby police station," Amanullah, Bukhari's official spokesperson told a news agency.
Some drops of kerosene fell on Bukhari's clothes and some on the floor, but nobody was hurt, police said.
During interrogation, Kamaluddin told police that he wanted to meet the Imam and when he could not get through, he threw the bottle.
"He had reached Delhi yesterday via train and had tried to meet Bukhari several times. But when he couldn't get through, he got miffed and procured a bottle of kerosene and threw on him," Joint Commissioner of Police(Central) Sandeep Goel said.
We are trying to establish as to why he wanted to meet Bukhari but so far his utterances have not been very coherent, Additional Commissioner of Police (Central) Alok Kumar said.
"We have also found a match box and a lighter from him. We would book him for attempt to murder," Goel said.
Sources said that the man was also interrogated by the Special Cell of the Delhi Police and intelligence agencies and efforts are on to establish his antecedents and also that he appeared to be mentally unstable.
The incident, which took place inside the premises of the 17th century Jama Masjid raised questions over its security as the man managed to carry a bottle of inflammatory substance inside the monument.
Door frame metal detectors have been established on all the entrance gates of the mosque which are manned by armed Delhi Police personnel.
On Sunday, 19-year-old Shaban Bukhari, son of Imam Syed Ahmed Bukhari, was chosen to succeed his father as the 14th Shahi Imam of Delhi's Jama Masjid, the largest mosque in the country.
(With PTI inputs)