Briton Froome was with Australian Richie Porte and Bauke Mollema of the Netherlands when all three crashed into a motorcycle that was halted because of fan overcrowding.
During the three-week race, which covers 3,500 kilometers, millions of spectators line the route and on the summit finishes, where the race is effectively decided, thousands of avid fans camp out for days to find a viewing spot ahead of the peloton's fleeting arrival.
Froome's compatriot Adam Yates temporarily grabbed first place as a result of the crash -- although the defending champion's leading position was later restored after the incident was deemed a result of extenuating circumstances.
Froome did not appear to be injured after Thursday's collision, but he quickly realized his bike wasn't up to the job anymore if he was to reach the finishing line.
So while waiting for his team to bring a new bike, Froome ran up Mont Ventoux's steep incline, before hopping on a neutral bike -- which he found unusable -- and then finally on a team bike to finish the twelfth stage.
Froome dropped from first to sixth place as a result of the setback, and had trailed 23-year-old Yates by 53 seconds in the provisional standings before the decision was reversed.
"The motorcycle couldn't pass because of thousands of fans," Froome's sports director at Team Sky Nicolas Portal told reporters. "It's not one, two or 10, but for 200 meters there were hundreds of fans."
Froome's main rivals, including Colombian Nairo Quintana, were also held up by the crash as a throng of fans obstructed the road.
Porte hit the motorbike with Froome next and Mollema also running into the back of the vehicle.
Six-time Olympic cycling champion Chris Hoy tweeted: "Something has to done re the crowd control, it's beyond a joke."
But the lasting memory will be one of Froome running uphill for the final kilometer in a desperate attempt not to lose valuable time.
It's not the first time this year's Tour, the 103rd edition of cycling's most famous race, has encountered organizational problems.
On stage seven the inflatable arch indicating the race's final kilometer has been reached deflated, bringing down Yates, as he passed beneath it.