Ukrainian officials said another three people were killed in Russian strikes elsewhere in the country, and Moscow claimed fresh advances on the ground.
Russia frequently targets Kyiv with aerial attacks, but deadly strikes there are rare as the capital is heavily protected by air defences and better able to fend off attacks than elsewhere in the country.
Ukraine's President Volodymyr Zelensky called on the world to step up pressure on the Kremlin to force it to end the nearly three-year invasion.
City officials said the victims were two men, aged 43 and 25, and a 41-year-old woman.
AFP journalists in Kyiv saw a multi-storey building with windows blown out, debris strewn across the street, flooding, and the charred facade of a damaged McDonald's outlet.
Russia's defence ministry said its forces had "carried out a group strike with precision-guided weapons against Ukrainian military-industrial facilities, including the Luch Design Bureau that develops and manufactures long-range guided missiles".
The attack on the target in Kyiv was "retaliation" for Ukraine's use of US-supplied ATACMS missiles in strikes on Russian territory, it added.
At least three people were killed and three wounded, Zelensky said, revising down an earlier toll of four.
"Everyone who is helping the Russian state in this war must be put under such pressure that it is felt no less than these strikes," Zelensky said on social media.
Later Saturday, in his evening address, Zelensky noted that the strikes had been carried out by ballistic missiles.
"We are constantly working to secure more air-defence systems for Ukraine -- modern systems -- capable of intercepting these types of ballistic missiles," he added.
- 'Heinous Russian attack' -
Calling it a "heinous Russian ballistic attack", Ukrainian Foreign Minister Andriy Sybiga said it was "yet another proof that Putin wants war, not peace".
The Russian president "must be forced to accept a just peace through strength -- maximum economic and military pressure", he added.
Ukraine's air force said it had downed two Iskander ballistic missiles as well as 24 Russian attack drones overnight.
They had fallen on Kyiv's central Shevchenkivsky district, damaging an industrial building, an entry to the metro and residential buildings, as well as temporarily knocking out local water supplies.
In the southern city of Zaporizhzhia, one person was killed and 11 wounded in a Russian strike, its governor, Ivan Fedorov said, describing it as "cynical" attack on the city centre "while everyone was sleeping".
And another two people were killed in a mortar attack on Beryslav, in the southern Kherson region, its governor Oleksandr Prokudin reported.
These latest strikes come at a critical juncture in the conflict.
Both sides have been seeking to secure the upper hand in the conflict ahead of US President-elect Donald Trump's inauguration on Monday.
Russia on Saturday claimed its forces had captured two villages -- Vremivka and Petropavlivka -- in the eastern Donetsk region, where its troops have been grinding forwards for months.
Ukraine has launched a wave of strikes against Russian energy and military facilities, including sites hundreds of kilometres behind the front lines.
Its GUR military intelligence unit said Ukrainian drones had hit an oil depot in Russia's Tula region in the early hours of Saturday.
The Russian governor of the region had earlier reported a fuel tank fire at an industrial site in the region after a Ukrainian drone attack.
In the neighbouring Kaluga region, officials also reported a fire at an industrial site, apparently another oil depot, after a Ukrainian drone attack.
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