Khan was produced before Duty Magistrate Harjit Singh Jaspal at his residence during late hours on Friday.
He will now be produced before a Prevention of Money Laundering Act (PMLA) court later in the day.
Khan was arrested by Delhi Police from New Delhi Airport on his arrival from Dubai.
"Khan was taken into custody on landing at the New Delhi international airport on arrival from Dubai around 2 a.m. in an Air India flight 916. He will soon be brought to Bengaluru by our sleuths," SIT officer Mohammed told here.
The major breakthrough in the IMA Gold multi-crore cheating case for the Enforcement Directorate (ED) and the SIT came as a lookout notice on Khan was issued to all concerned, including the Interpol, through the Union Home Ministry.
Khan, who is accused of perpetrating financial fraud worth crores in Bengaluru, was absconding for a month and was traced in Dubai and told to return to India.
"He had shared a video in which he claimed that he shall return to India in next 24 hours," the SIT officer said on its basis the arrest was made.
"Our officer will take Khan's custody from the Delhi Police and fly him back to Bengaluru according to procedures for investigation into the mega scam," added Mohammed.
The development is expected to ease the ongoing investigation and the effort to return the money of thousands of investors.
( With inputs from IANS )