The demolition work was being carried out under heavy security arrangement, in the presence of a 300-member strong squad, comprising policemen and civic officials, sources said.
A Maharashtra Control of Organised Crime Act (MCOCA) court, which is seized of the matter, has approved the demolition while rejecting the plea made by one of the accused seeking a stay on the demolition of the shopping complex on the ground that the structures are vital piece of evidence and the trial is in progress.
Dawood's brother Iqbal, who was extradited from Dubai, is also facing the trial.
The complex stands on a plot of land owned by Central Public Works Department and was illegally built in connivance with municipal officials, according to police.
The Bombay High Court had earlier upheld the order of a lower court allowing demolition of illegal complex allegedly set up by the don.
The tenants of the complex filed an appeal in the Supreme Court which upheld the High Court order.