Scores of demonstrators, including young children, shouted "No justice, no peace," and "Stop shopping and join the movement" at the St Louis Galleria Mall on Friday.
Around 100 people lay on the floor for four and a half minutes to symbolise the more than four hours that 18-year-old Michael Brown lay in the road after being shot dead by a white police officer in the St Louis suburb of Ferguson.
In New York, police made "several" arrests at a protest in front of Macy's flagship store in Herald Square, a spokesman said, without explaining why the demonstrators had been detained.
About 200 people gathered in support of the boycott of Black Friday, which comes the day after America's Thanksgiving holiday and sees stores offering steep discounts, leading to often-frenzied consumer spending.
In the San Francisco Bay area, protesters severely disrupted the BART mass transit system for more than two hours by blocking off a train station in Oakland, officials said.
The protesters chained themselves together at the West Oakland station, forcing trains to be stopped into and out of San Francisco, briefly stranding crowds including many heading to malls seeking Black Friday bargains.
The protests came four days after a Missouri grand jury decided not to indict the officer who killed Brown, sparking arson and looting in Ferguson.
At the St Louis mall, shoppers and store staff looked bemused, while others filmed or photographed the protest, or else clapped and shouted their support.
When police officers told AFP they were clearing the building, the protesters had already left.
The management office confirmed that the shopping centre reopened around two hours after stores were told police were closing the building.
Although most shops reopened, others kept their doors locked and shutters down even after the mall was back in business.
It was not immediately clear how much business had been lost.
Shop staff said police had ordered the closure for public safety.
"It ain't my decision," said Luke, a shoe store manager who didn't want to give his last name.
"The police thought it was in the best interest of our customers and our product to close down," he added.
Protesters claimed success.
"It is now a movement and it is spreading across the country and around the world. Black Friday is the next step," said journalist and activist Kymone Freeman from Washington.
"Hopefully we'll see more of this. I think Black Friday protests will continue throughout the Christmas season."
