Sheik Hassan Mussa, imam of the Södermalm mosque, deplored "all forms of attacks, violence, fears and threats against innocent people, whatever the motive or pretext", in a statement sent to the Swedish news agency TT.
The security and stability of Sweden are a religious and social duty, he added.
The explosions in a busy part of the capital packed with Christmas shoppers came minutes after Sweden's TT news agency received a message denouncing Sweden's military presence in Afghanistan and threatening deadly attacks.
Foreign Minister Carl Bildt spoke of a "terrorist attack" that could have had "catastrophic consequences" and Sweden's secret service called the blasts a "terrorist crime".
The suspected bomber is believed to be the lone fatality in the blasts, which injured two other people.
On Sunday, a spokesperson for Swedish security service Säpo said the blasts were being investigated as a "terrorist crime", adding however that it was "too early" to say for sure whether or not there is a connection between the explosions and the message sent to TT.
The Swedish government is being updated continually as the investigation into the blasts proceeds, but still considers it a police matter.
Prime minister Fredrik Reinfeldt has no plans for a statement for the moment, his spokesperson Roberta Ahlenius told the TT news agency early Sunday morning.