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The Alpecin rider Philipsen finished at a speed over 67kph and took the overall lead in the sprint points battle after pipping Caleb Ewan and Phil Bauhaus.
British veteran Mark Cavendish came fifth as he continued to face frustration in his quest for a 35th Tour de France win to break the all-time record he shares with Eddy Merckx.
The 38-year-old, who finished sixth in Monday's sprint, and then said he picked the wrong wheel to follow.
In the shockingly accident-filled finish, the peloton sped around a motorbike racetrack where there was a string of crashes on the rounded chicanes.
Tour medics have confirmed two riders broke collar bones.
Adam Yates retained the overall leader's yellow jersey six seconds ahead of his teammate Tadej Pogacar and seven ahead of his brother Simon Yates.
The Tour's first massive mountain stage awaits the peloton Wednesday with around 30km of climbing at an average gradient of over 7 percent.