Six civilians, including a foreign woman, died at the Intercontinental Hotel in Kabul, along with three attackers, the interior ministry said.
Some 160 people were rescued after Afghan troops fought through the night to regain control of the building.
But some reports suggested gunfire had continued for some time after the authorities declared the siege over.
Afghan news agency Tolo says the death toll could be higher than the official figure, quoting a reporter who said they had seen dozens of bodies inside the hotel.
Afghan special forces were lowered by helicopters on to the roof of the hotel during the night, an interior ministry spokesman said.
They were working with Western special forces to bring the siege to an end.
Forty-one foreigners were among those rescued and seven people were wounded, according to figures from the interior ministry.
The ministry has promised an investigation into how the attackers breached security, which was handed to a private company two weeks ago.
Some reports suggest the gunmen entered the hotel through a back door in the kitchen.
Saturday's siege comes just days after the US embassy in Kabul issued a warning about hotels in the city.
"We are aware of reports that extremist groups may be planning an attack against hotels in Kabul," the embassy wrote in a public security alert published Thursday, though it highlighted another hotel near the international airport as a possible target.
"These groups may also be targeting public gatherings/demonstrations, government facilities, transportation, markets, and places where foreigners are known to congregate."
The Intercontinental is a state-owned hotel - not linked to the global hotel chain of the same name - which often hosts weddings, conferences and political gatherings.
Security has been tightened in Kabul since last May, when a huge truck bomb killed at least 150 people.
However, there have been several attacks in recent months. They include a bomb at a Shia cultural centre last month that killed more than 40 people.
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