Froome suffered a mechanical problem on the Mont du Chat, the last of three hors categorie climbs on the day, and as the three-time Tour victor was calling for the team auto Aru attacked in a clear breach of cycling's protocol.
Uran took victory in a photo finish ahead of Warren Barguil, one final twist of drama on a day that will live long in Tour history.
Rigoberto Uran of Cannondale has won a hugely dramatic Stage 9 of the Tour de France in Chambery on a day when second-placed Geraint Thomas of Team Sky and one of the big favourites for the overall win, BMC Racing's Richie Porte, both crashed out.
Thomas started the day 12 seconds adrift of Team Sky team-mate Froome in second spot in the GC standings, but his race was ended when he damaged his shoulder in a fall.
And the battle for the stage win came down to a slow-motion sprint between an exhausted group, containing Chris Froome in the yellow jersey.
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The Australian went slightly off the narrow road and crashed across the surface into a rock on the other side of the road, taking out Dan Martin in the process. "Richie will be taken to hospital for examination", said Porte's BMC team on Twitter. Organizers said he was conscious and speaking.
Thomas's race came to an end when he crashed on a corner while descending the Col de la Biche, with several riders in the break crashing at the same point shortly beforehand.
Earlier this season the Welshman had to leave the Giro d'Italia early after a crash involving a race moto.
The two-times Tour victor Alberto Contador also hit the deck as he fell on the ascent of the Grand Colombier, but the Spaniard was quickly back on his way with a push from spectators.
The defending champion, who was attacked by Fabio Aru (Astana) just as he suffered a mechanical on the last climb, crossed in third.