The Al Umma was responsible for 11 deaths in an explosion at the RSS building in Chennai in 1993.
Bengaluru police commissioner Raghavendra H Auradkar said the arrested had been identified as Basheer alias Sunnati Basheer, Peer Mohideen and Kichen Bhuhari alias Bhugari. He declined to comment whether they belonged to any terrorist group.
The police caught the scent of the suspects though mobile text messages of Basheer, who had sent an SMS about the blast to his aide on April 16, saying: "Let us carry out the bomb blast in Bangalore. Come to Shivajinagar."
Other than the motorcycle, it was the design of the bomb that led the police to Madurai, where activists of the banned organisation had planted a similar crude bomb on the route BJP leader LK Advani was to take two years ago.
An analysis of the motorcycle, a Suzuki Samurai with a fake number plate, its engine and chassis numbers enabled the police to trace the original owner, a software engineer of Chennai.