The Ahlens department store apologised "for a bad decision" in a statement on its Facebook page.
It said its motivation "was born out of the idea of standing up for transparency and not allowing evil forces take control of our lives."
The store said it would reopen tomorrow "without any damaged goods."
A fire broke out Friday afternoon at the store after the truck smashed into shoppers at its entrance on Stockholm's pedestrian Drottninggatan street.
Police have arrested a 39-year-old native of Uzbekistan and say they believe he deliberately drove the truck into shoppers.
Overnight, Swedish media reported police raids to bring other people in for questioning as authorities investigated the deadliest attack in Stockholm in years.
Sweden's SAPO security police said it was working to find "any abettor or network involved in the attack."
"We have a lot of people who are being taken to police offices throughout Stockholm for questioning," police spokesman Kjell Lindgren told The Associated Press.
"But no one has been put into custody or arrested" beside man from Uzbekistan.
Stockholm city officials, meanwhile, planned to move thousands of flowers at a makeshift memorial to a nearby square after an aluminum fence outside the Ahlens department store was overwhelmed with tributes and threatened to collapse, Sweden's TT news agency said.
The fence was put up to keep people away from the broken glass and twisted metal at the attack site, and to allow forensic experts and police to gather evidence.
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