Belgium remains on a high state of alert after Islamic State-claimed bomb attacks in March left 32 people dead at the airport and at a metro station near European Union headquarters buildings.
Prosecutors said they were still investigating whether the man - who had once claimed he had been urged to join the Islamic State group in Syria - had any genuine links to terrorism or not.
"After an initial inspection it was confirmed that it contained salt and biscuits. Any threat of an explosion has been initially ruled out," prosecutor's spokesman Rym Kechiche said in a statement.
"JB is known to the authorities for various incidents, including some linked to psychiatric problems," Kechiche said.
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Police later located the car identified by the suspect in the Schaerbeek district of the capital and planned to question its owner.
Only one exit remained open at the nearby Rogier metro station, where soldiers checked passengers bags and belongings. Police and soldiers sealed off the immediate area, an AFP reporter at the scene said.
Prime Minister Charles Michel called an emergency meeting of his security cabinet when the shopping mall alert was ongoing, reflecting the tensions in the country.
"The situation is for now under control. We remain vigilant," Michel said after the meeting.
The terror alert level in Brussels remained at level three out of four, Belga news agency reported.
The City 2 mall had been mentioned in Belgian media in recent days as a possible target for attacks.
Authorities said at the time they were responding to a need for "an immediate intervention".
The areas searched included neighbourhoods in Brussels where November's jihadist attackers in Paris and the Brussels suicide bombings had planned their assaults.
In proportion to its population, Belgium has the highest number of so-called foreign fighters in the EU who have travelled to wage jihad in Syria and Iraq, an estimated 500.