The race remains wide open as the Tour heads into the tricky alpine stages 17 and 18 - with just half a minute separating the top four riders.
Irishman Dan Martin was one of the highest profile losers of the stage.
Martin's team-mates seemed to be more interesed in helping Marcel Kittel hold onto the green jersey rather than assist the Irish rider who may have seen his yellow jersey chances disappear today.
Froome leads the Tour, the closest in history at this stage in the race, by 18 seconds from Italian national champion Fabio Aru, with Frenchman Romain Bardet a further five seconds back. Edvald Boasson Hagen (Dimension Data) finished second in a photo finish, with John Degenkolb (Trek-Segafredo) in third.
German Marcel Kittel, who was dropped early in the stage after failing to sustain the pace in the first climb, was 3.2kph slower on average than Australian stage victor Michael Matthews. "I left a space between me and the barrier", Matthews said, adding that Degenkolb had grabbed him by the neck after the finish.
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But German Degenkolb was angered by the line Matthews took in the finish and waved his hand at the Aussie as they crossed the line.
"I saw the sprint on TV afterwards".
Matthews collected points in the intermediate sprint and at the finish to narrow the gap with Kittel to 29, setting up a duel with the Quick-Step Floors rider in the final days of the race. "I called the boys and they came to the front with big smiles on their faces and went full gas". "I think it won't sink in until tomorrow morning".
Chris Froome retained the overall lead in a hectic finale baulked by crosswinds that saw top 10 contenders Daniel Martin, Louis Meintjes (both 51sec) and Alberto Contador (1min 33sec) lose time.
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