Keukeleire hit the ground in the same accident that saw BMC's Richie Porte forced out of the race with a broken collarbone on Sunday.
While Porte was said to have crashed after just 10 kilometres, Lotto Soudal stated that Keukeleire had crashed "after only 15 kilometres of racing". Either way, it was early on the stage, and well ahead of the day's first sector of cobbles, which came just under 50 kilometres into the 156.5km stage.
And it was definitely the same crash, as Keukeleire confirmed.
"Everyone was talking about the nervousness and the cobbles on Sunday, but the crash, in which among others Richie Porte and I got caught up, had nothing to do with that. Michael Valgren had a chain problem and that caused the crash," explained Keukeleire in a team press release.
It was confirmed by BMC shortly after the crash that Porte's injuries were forcing him to retire, while Astana's Valgren was able to remount and finish the stage, and was even later seen at the front of the race helping his team leader Jakob Fuglsang.
Keukeleire, too, was able to finish the stage, down in 142nd place, more than 16 minutes behind stage winner John Degenkolb (Trek-Segafredo). But Lotto Soudal waited until they had the results of an MRI scan before making a decision as to whether 29-year-old Keukeleire would be able to continue.
The team announced on the Tour's first rest day in Annecy on Monday that, having received the result of the scan, Keukeleire would be heading home and not starting Tuesday's 10th stage from Annecy to Le Grand-Bornand.
"Jens has a fracture to the upper part of his fibula, and his thigh is bruised," said team doctor Servaas Bingé. "Because of a straining of the ligaments, his knee is unstable, and that makes racing impossible. We drained the superfluous blood to remove the swelling, but that didn't turn out to be the solution. Starting the stage is not an option.
"Jens will be wearing a brace for the next two weeks," Bingé continued, "and for the next four weeks he won't be able to do any strenuous exercise."
Keukeleire added about his injury: "Of course my knee hurt, but it was only after the stage that it started to swell.
"I came to the Tour to forget about my spring, which was also full of bad luck," he said, referring to the fact that he missed most of the spring Classics due to illness.
"Therefore it's such a shame that I need to abandon the race. It's too early to make new plans, but I hope to be able to race in the last part of the season, and to have a good winter afterwards."