The overall standings remained unchanged at the top with Thomas leading defending champion Froome by one minute 39 seconds and Dutchman Tom Dumoulin by 1:50.
New coronavirus cases have been rising at an alarming rate in France since the beginning of the month, casting a menacing shadow over the re-scheduled 107th edition of the race.
Norway's Kristoff outsprinted Danish world champion Mads Pedersen after 156 km around Nice.
Stage eight winner Nans Peters had long crossed the line when fellow Frenchman Thibaut Pinot's ordeal ended after the Groupama-FDJ rider, highly fancied to become the first local winner of the race in 35 years, had been dropped in the second ascent of the 141-km trek through the Pyrenees.
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