Organisers said that Thomas, who went down on the slippery descent from the Col de la Biche, had retired from the Tour. "More updates when we have them".
Thomas was second overall at the start of the day, just 12 seconds behind reigning champion and his Sky team leader Froome. The 31-year-old won the opening time trial of the Tour in Düsseldorf and held the yellow jersey until stage five.
It's been an unfortunate year for Thomas, who also exited the Giro d'Italia in May following a crash caused by a police motorbike.
Three riders from the day's break - Movistar's Jesus Herrada plus Alexey Lutsenko and Bakhtiyar Kozhatayev of Astana - had crashed on the same corner as Thomas minutes before the peloton arrived.
It was Thomas's fourth crash of the Tour, having also gone down on the second, fourth and eighth stages.
Two-time 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.