With a kilometre to go, Froome took the lead of a group of six but was beaten in the sprint as Rigoberto Uran (Cannondale) held off Warren Barguil (Sunweb) and Froome to win the stage.
Worse was to follow for pre-Tour favourite Richie Porte on the final descent, with a horror crash involving him and Ireland's Dan Martin forcing the Australian to abandon.
Porte, seen as one of the main rivals to his Sky team-mate Chris Froome, was taken to hospital, his tour over at the end of the first week.
Baldato added that Porte had ridden the descent four times before the Tour, including once in racing conditions during last month's Criterium du Dauphine. He came off his bike and skidded across the tarmac into Martin, clattering both into the rock face on the other side of the road.
Martin remounted but was involved in another crash shortly afterwards, while Porte, widely regarded as the biggest threat to Froome's title defence, received treatment for nearly half an hour at the roadside before being taken away in an ambulance.
"He was conscious, it's reassuring, he is being transferred to the hospital", Pommery said.
A very hard day on the mountains saw Froome need a bike change but recover to take a commanding lead in the Tour as Porte and Thomas crashed violently.
Thomas went down on the slippery descent from the Col de la Biche and Team Sky say he has suffered a suspected broken collarbone.
Earlier this season the Welshman had to leave the Giro d'Italia early after a crash involving a race moto. "After I caught Nairo (Quintana) at the bottom, everyone was committed and it was just a case of getting to the finish". He is now sixth overall, 1:44 minutes behind Froome, who claimed a third-place finish on the stage.