Pubs in five healthboard areas, including Glasgow and Edinburgh, will have to close for a 16-day period from Friday 9 October.
The health boards cover Greater Glasgow and Clyde, Lanarkshire, Ayrshire and Arran, Lothian, and Forth Valley.
In other parts of the country, venues will only be able to operate indoors on very restricted basis between 6am-6pm, serving food and non alcoholic drinks only.
Pubs can still serve alcohol outdoors.
There is an exemption for occasions marking life events, such as weddings or funerals.
Sturgeon called these measures "tough but necessary actions".
She said she wanted to be "honest" with the sector, not put them in a position where they were "all but closed" and lacking financial support. The Government will consult the hospitality sector on additional financial support this week.
An additional £40m would be made available to support businesses affected by these measures, the minister said in her Holyrood briefing.
She added: "The reason we are not closing indoor hospitality completely is that we know the benefits, in terms of reducing loneliness and isolation, of giving people - particularly those who live alone - somewhere they can meet a friend for a coffee and a chat."
While the majority of pubs and bars were working hard to protect public health, Sturgeon said pubs "inevitably" presented a transmission risk.
She said: "Indoor environments, where different households from different age groups can mix, inevitably present a risk of transmission.
"That risk can be increased in some hospitality premises if good ventilation is difficult, and if it is hard to control the movement of people.
"And the presence of alcohol can of course affect people's willingness to physically distance."