As a result, Froome was forced to run up the iconic Mont Ventoux without a bike because his team and their spares, were miles behind.
In a complete embarrassment for race organizers on Bastille Day, Richie Porte crashed into a motorbike carrying a TV camera and Froome, who was following right behind his former teammate, also crashed in the final kilometre on the wind-shortened climb to Mont Ventoux.
Froome picked himself up and could not find his bike and so there was the freakish sight of the yellow jersey wearer running up the road.
He ran as fast as his cycling shoes would carry him before taking a bike from the neutral service auto, but struggled to gain traction on the ill-fitting machine and had to swap it again when his team vehicle finally made it through.
Six-time Olympic cycling champion Chris Hoy tweeted: "Something has to done re the crowd control, it's beyond a joke".
"I'm very happy with the commissaires' decision, I think it was the right thing to do, thanks to the jury and thanks to the organisers", Froome told reporters.
Spotting a chance to gain time on his rivals for the general classification, Froome followed with compatriot Thomas and the foursome soon opened up a lead that stretched out to a maximum of 26 seconds.
To prevent fans and cyclists from blowing over at the top of the challenging 6,300 foot high peak of Mont Ventoux, Tour de France officials made the decision to change where the finish line was for Stage 12.
As Froome ran through the crowds, he attempted to communicate with his team with his radio - but the crowds prevented the Team Sky assistance vehicle from reaching him.
Froome retains Tour de France lead despite Ventoux chaos
The Orica-BikeExchange rider acknowledged the strength of Chris Froome on Wednesday, approximately half an hour after the race leader extended his lead by 12 seconds.
Froome was caught in the accident and his bike was damaged, but the Team Sky auto was well behind him.
The two-time Tour victor eventually got a replacement bike and crossed the line way behind Mollema and Porte in a time that would have handed the yellow jersey to young Briton Adam Yates.
"I don't know what to expect, if anything it's going to mean an even more intense race before we hit the climb because it's going to be shorter".
"I was just riding up behind the favourites group and I had a gendarme basically stiff-arming people out of the way just to keep me upright". The guys went straight into me.
Froome had finished nearly two minutes behind Adam Yates.
Giving Porte and Froome the same time as Mollema, who remounted quickly after the crash to snatch a top-ten finish behind the breakaway, was - on reflection - the fairest decision. He is now 31 seconds ahead of Dan Martin (Etixx-QuickStep) and a further four seconds up on Nairo Quintana (Movistar).
News coverage showed footage of a rider slamming into a cameraman, and photos posted to social media show fans standing dangerously close to the course holding signs.