The visit drew a sharp rebuke from authorities in Kiev, who accused the Russian strongman of stoking tensions with his visit to Sevastopol, home to Russia's Black Sea fleet.
"This provocation once again confirms that Russia deliberately seeks further escalation of tensions," the foreign ministry said, calling the visit a "flagrant violation of Ukraine's sovereignty".
The White House also condemned the trip, with National Security Council spokesman Laura Magnuson saying it "will only serve to fuel tensions".
An attempt by around 60 rebels armed with automatic weapons to storm the city's police headquarters turned into a "full-scale military clash" when army and interior ministry troop reinforcements arrived, Interior Minister Arsen Avakov said on his official Facebook page.
He said the death toll from the near-two-hour combat stood at 20 rebels and one policeman, while another four policemen were wounded and four rebels were captured.
Witnesses in Mariupol told AFP the fighting was ferocious and involved an exchange of automatic gunfire and shelling from eight armoured vehicles.
"There was an awful lot of shooting," said an eyewitness who gave his first name as Aleksandr.
In Sevastopol, Putin reviewed Russian ships in the bay, hailing the sailors on board with a "Hello comrades!" as he congratulated them on the 69th anniversary of the Soviet victory over the Nazis in World War II.
Putin said 2014 "will go down in history" as the year when the "historic truth" of Crimea as part of Russia was recognised.
"Much work remains ahead, but we will overcome all difficulties... Because we are together. And that means we are even stronger," Putin told a cheering crowd.
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