He beat France's Warren Barguil of Team Sunweb after a photo finish.
And yet the Tour had started so well for the 31-year-old Briton, who won the opening stage time-trial, his first ever Tour stage victory, and held the yellow jersey for four days before giving it up to Froome on Wednesday's fifth stage.
Australian Richie Porte crashed spectacularly out of the Tour de France on a treacherous and costly ninth stage Sunday. He careened across the road and clattered into Ireland's Dan Martin, bringing the two crashing into the rocky side of the road in the final 25 kilometers of the 181.5-kilometer stage from Nantua to Chambery.
While Porte quickly received medical attention on the track, Martin was able to dust himself down and continued racing. Organizers said he was conscious and speaking.
"He had a lot of pain but we need to wait for the doctors", he said.
Martin crashed first in the incident that saw Richie Porte abandon the race, and then again shortly after when his brakes didn't work with a replacement wheel.
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Overall, Froome leads Aru by 18 seconds and Romain Bardet by 51 as two-times victor Alberto Contador of Spain cracked on the last climb and dropped out of contention.
"I want to thank the other riders, who did not attack", he added, saying he did not see Aru attacking past him as he raised his arms to ask for assistance.
He also went down in the second, fourth and eighth stages.
After picking himself up, Martin finished in a group including Movistar's Nairo Quintana and Orica-Scott's Simon Yates, one minute and 15 seconds behind the leaders. It was a big occasion for me after so many things happened today like the crash of Richie Porte. "I managed to catch the group in front of me after I crashed the second time - I was flying down the mountain", he said with a smile.
Monday is a rest day for the riders.