The Welsh rider, who took the overall lead after last week's opening time trial in Dusseldorf, had been second overall at the start of the stage, 12 seconds behind team leader Chris Froome.
He lay motionless on the road for some time, being attended to by medics before being taken to hospital, although organisers said he was conscious and speaking.
Frenchman Romain Bardet (Ag2R-La Mondiale) and Astana duo Aru and Jakob Fuglsang completed the top six before a chasing group including Colombian Nairo Quintana (Movistar) came home one minute 15 seconds down.
The Col de la Biche was the first of three hors categorie climbs to be tackled on a brutal day of racing through the Jura mountains.
After numerous attacks including from Aru and Porte, Froome dropped the other GC rivals, with Nairo Quintana (Movistar) and Aru unable to stay with the three-time Tour de France victor.
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Each cut has come after various United Nations bodies voted to adopt decisions which Israel said discriminated against it. As Palestinians gathered to pray, Goldstein opened fire inside the compound, killing 29 people including children.
In the confusion that followed, Bardet used his local knowledge of the roads to ride clear and catch his compatriot as the road levelled out in the run into Chambery.
Getting through Sunday's Stage 9 unscathed, arguably the toughest of this Tour's 21 stages, marked a crucial step in the three-time champion's campaign for a fourth win.
If Quintana - 2:13 down in eighth place - kept his faint hopes of a first Tour crown alive, then the same can not be said of Contador: the former double Tour champion is now more than five minutes down on Froome in the GC.
Monday is a rest day and the fight for the overall title is set to resume next Thursday with the first big Pyrenean stage.
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