In the trendy district of Södermalm, the authorities ordered Carmen, Charles Dickens, The Central Bar, and Raw Sushi & Bowl to close, while in upmarket Östermalm, they shut the International Bar. Two other bars were reported but allowed to stay open.
The closures came as Sweden's statistics agency reported that the second week of April witnessed its highest death rate since the turn of this century, underlining the price it has paid for its decision not to impose a lockdown.
Sweden has so far reported 2274 virus deaths and almost 19,000 cases, putting its per capita death rate from the pandemic at more than triple that of neighbouring Denmark and nearly six times that of Norway and Finland, all of which put in place heavier restrictions.
Yesterday's closures mark the first departure from the country's soft-touch approach to social distancing.
"We can't legislate and ban everything. It's also a question of common sense behaviour," Stefan Löfven, the Prime Minister, said at the end of March, as Sweden laid out its recommendations.
The country's authorities have allowed cafés, bars and restaurants to stay open throughout the crisis, with the proviso that they only provide table service and that they space tables between 1 to 2m apart to prevent overcrowding.
The closures in Stockholm followed rising concern that Swedes' socialising was reverting to normal, with reports of crowded pubs, cafés and parks in recent weekends.
Ioana Caraman, a Stockholm resident from Romania, said that when she had been out in the city's upmarket Östermalm district on Friday night, the crowds had been the same as before the crisis.
"We were there about 9pm, which is early for Östermalm, and it was crazy full," she complained. "The queues were really long and we couldn't get in anywhere. They really don't keep the space between people like they should. There's really no social distancing in Sweden at all."
"Everything is almost the same," said Hakan Dinçer, who works in a bar on the island of Kungsholmen. "The place was full until 3am on Friday, and on the previous weekend as well."
Katarina Luhr, a Stockholm city councillor, said that the authorities had received hundreds of complaints over the weekend from worried citizens.
Anna König Jerlmyr, Stockholm's Mayor, warned the country's pubs and restaurants: "The restrictions are not just tips; they should be followed."