Dozens of riders fell victim to the saboteurs who threw small nails on the ground near the top of the Mur de Peguere climb, 38 km from the finish, and caused several leading riders to puncture.
Defending race champion Cadel Evans among the first victims. He initially lost over two minutes waiting for a spare wheel.
The Australian, who suffered three punctures in total in the finale, managed to latch back on to the peloton thanks in part to the work of his BMC team but also down to the sporting behaviour of the peloton.
Once the extent of the incident became apparent, the Sky team of yellow jersey holder Bradley Wiggins helped restore order by waiting for those delayed riders affected by the sabotage.
Wiggins himself had to change bike due to a puncture.
"Whether it was aimed at someone or something I don't know. It's sad, but those are the types of things we have to put up with as cyclists," said the Briton, who leads Sky teammate Chris Froome by 2min 05sec going into the 15th stage.
Tour de France organisers immediately lodged a formal complaint with police.
A statement by race organisers ASO (Amaury Sports Organisation) said "management of the race has decided to lodge a formal complaint with police".
It added: "We condemn this irresponsible and dangerous behaviour, which amounts to an attempt to harm the physical integrity of the riders and the smooth functioning of the race".
The public prosecutor in Foix later announced it had opened a preliminary investigation into the incident.
"The investigation will be taken over by special branch from the Toulouse and Saint Girons gendarmerie. They have been sent to the site to collect statements and testimony from witnesses," Marilyn Blanc, the vice-procurator, told AFP.
Blanc said that testimony may also be taken from the riders who fell victim to the incident.
It is not the first time the peloton or specific riders have been targeted by one or several spectators at the side of the road.
Belgian cycling legend Eddy Merckx was once punched in the stomach by an angry spectator in the 1975 Tour de France.
Several years ago some riders in the peloton fell victim to teenagers shooting air rifles. New Zealander Julian Dean was one of the riders hit with pellets.
Evans admitted on Sunday he now rarely races in Spain, after effectively losing the Tour of Spain title when he punctured on suspect material thrown on to the road.
"For that reason I don't race in Spain very often. It's cost me a Vuelta (Tour of Spain), it's cost me other races," said the Australian.
Wiggins, meanwhile, said cyclists offering the fans a free spectacle on the road should not be taken for granted.
"I think people take that for granted, just how close they can get to us," he added.
"If that happened in a football stadium you'd be arrested, (thanks to) CCTV, but we're out there and we're quite vulnerable at times, very close to the public.
"We're just the riders at the end of the day, and we're there to be shot at, literally. So it's quite sad and hopefully that's not going to continue."