The £38m yacht, named Phi, is owned by an unnamed Russian businessman, but the government said its ownership is “deliberately well hidden”.
Transport secretary Grant Shapps said the move was “a clear and stark warning to Putin and his cronies”.
The UK has already introduced a raft of sanctions against Russia following its invasion of Ukraine.
Phi was first identified as being potentially Russian-owned on 13 March, the government said.
It added that the company the ship is registered to is based in the islands of St Kitts and Nevis but it carried Maltese flags to hide its origins.
The 58.5m (192ft) long yacht is the third biggest built by shipbuilder Royal Huisman and includes what the builders call an “infinite wine cellar” and as well as a fresh-water swimming pool.
UK officials boarded Phi in Canary Wharf, east London on Tuesday. The vessel was in the capital for a superyacht awards ceremony and was due to depart at 12:00.
The Department for Transport worked with the National Crime Agency and Border Force Maritime Investigation Bureau to identify and detain the vessel.
The department, alongside law enforcement agencies, are also looking at a number of other vessels.
The UK, US and EU have all said they will target superyachts linked to sanctioned Russians, and at least eight have been seized so far – by authorities in France, Italy and Spain.
For example, at the beginning of March French authorities seized a yacht owned by Igor Sechin, boss of Russian state energy company Rosneft.
More yachts remain on the move or moored in places that are currently beyond the reach of sanctions, including the Maldives.
Transport Secretary Grant Shapps said: “Today we’ve detained a £38m superyacht and turned an icon of Russia’s power and wealth into a clear and stark warning to Putin and his cronies.
“Detaining the Phi, proves, yet again, that we can and will take the strongest possible action against those seeking to benefit from Russian connections.”