The first man was found under some debris and was transported to an area hospital where he was later pronounced dead from his injuries.
This footage, showing the Amazon facility, was taken by videographer Vincent Figueroa.
The Amazon Fulfillment Center was one of several buildings to suffer from storm-related damage.
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Firefighters then worked through the night to try to locate a second person who was reported missing. That caused concrete panels along a 50-foot (15-meter) section of wall to collapse.
Baltimore Fire officials say Israel Espana Argote and 54-year-old Andrew Lindsey were killed after heavy wind and rain led to the collapse of a 50-foot wall at the Amazon Fulfillment Center in southeast Baltimore. The safety of our employees and contractors is our top priority and we have safely evacuated the building. Our thoughts and prayers go out to the families impacted by last night's tragic event, ' the spokesperson added.
The National Weather Service confirmed Saturday that the city's storm damage resulted from an EF-1 tornado.
It left a track of intermittent damage, flipping over a tractor-trailer, ripping down part of the warehouse, and tearing off the roof of a nearby apartment complex in Dundalk, he said.