Italian national champion Fabio Aru proved the most decisive of the contenders for the yellow jersey, making the most of the final kick up La Planche Des Belles Filles to escape from the other candidates for overall victory. His bold attack from 2.3 kilometres out took the long train of Team Sky by surprise and by the time the other favourites reacted, it was too late to make up the gap.
Aru powered clear to take the Stage 5 win by a margin of 16 seconds over Daniel Martin (Quickstep Floors) with Froome a further four seconds back.
The result puts Froome into the maillot jaune, with his advantage sitting at 12 seconds to his teammate Thomas, with his nearest rival Aru at 14 seconds and Richie Porte (BMC Racing) 39 seconds in arrears.
As it happened
The stage began as a flat affair with the looming spectre of the ascent of La Planche des Belles Filles on the horizon. Whilst a short climb, it is brutal in gradient with its varying nature certain to cause problems for all but the strongest of climbers.
A strong group of riders including Mickael Delage (FDJ), Edvald Boassen Hagen (Dimension Data), Phillipe Gilbert (Quickstep Floors), Thomas De Gendt (Lotto Soudal), Thomas Voeckler (Direct Energie), Jan Bakelants (AG2R La Mondiale), Dylan van Baarle (Cannondale-Drapac) and Pierre-Luc Perichon (Fortuneo-Vital Concept) went clear shortly after the flag fell at the start of the race.
Tsgabu Grmay (Bahrain-Merida) tried valiantly to get across until his team car came alongside and advised him that he that any further efforts to go across were futile.
The eight-man break continued pressing their gap out to a maximum of three and a half minutes before BMC Racing came to the front of the peloton, clearly confident in their leader, Richie Porte, and his ability to win the stage.
The break passed through the intermediate sprint point with Boasson Hagen taking out the top points, whilst back in the peloton there was a strong lead-out for Michael Matthews (Team Sunweb) who duly took out the sprint for the minor placings.
BMC kept the gap pegged to manageable levels, reducing the breakaway's advantage rapidly to just over two minutes, where it remained up until the final run-in to the climb of La Planche de Belles Filles.
Coming to the base of the climb, Gilbert broke away with Belgian compatriot Bakelants, with the two working together to delay the inevitable catch for as long as possible.
The pair were eventually caught with just under five kilometres remaining, as Team Sky took over pace-making duties on the front of the peloton sa the road tilted sharply upwards.
Michal Kwiatkowski and Mikel Nieve set a blistering pace for their leader, Froome, up La Planche des Belles Filles, shedding riders off the back until Aru launched a bold move with 2.3 kilometres to go. Simon Yates (Orica-Scott) went off the front to try and bridge to Aru, with the yellow jersey-wearer Thomas called on to catch the potentially dangerous move.
Froome reacted his own surge with 1.7 km left, with former teammate Porte glued to his wheel. The furious attack sent Thomas out the back, with only Martin, Porte and Romain Bardet (AG2R La Mondiale) able to follow his violent acceleration.
Aru showed his strength to maintain his advantage over the chase of Froome and once the British rider relented he continued to extend his lead. On the final viciously steep wall, Aru muscled his way over the top and took a win that would have sounded warning bells to the rest of the peloton.
Porte tried to launch an attack from behind in the final few hundred metres, but was overtaken by Martin and Froome on the run into the line, surrendering the chance to take a small advantage through the bonus seconds available at the finish.
Thomas ended up in 10th, finishing 40 seconds down on the stage winner and surrendering the leader's jersey in the process to Froome.