The incident took place in Noorbaug area in which Shabbir Ahmed Masiullah, 42, died.
His son Mahara Akram (11) was seriously injured and was being treated at a private hospital, said inspector S G Mandavkar of Ayesha Nagar police station.
As many as 31 persons were killed in a blast at Bada Kabrastan here in 2006.
Police initially arrested nine persons in the case, seven of them from Malegaon.
The National Investigation Agency, which took over the probe later, has said that Hindu right-wing activists were behind the blasts.