The Manxman, normally such a deadly finisher, hit the front several hundred metres from home after a strong lead out by Omega Pharma-Quck Step team-mate Gert Steegmans, but found himself overhauled by a rampant Kittel of Argos-Shimano, who won by half a wheel's length.
Green jersey Peter Sagan (Cannondale) was third ahead of Norway’s Alexander Kristoff (Katusha) and Italian Roberto Ferrari (Lampre-Merida). Yellow jersey Chris Froome (Team Sky) finished safely in the pack to retain his large lead on the general classification.
The long, flat 218km ride through the Loire Valley from Fougeres to Tours was marred by yet another big crash which ended the hopes of Kittel’s fellow German Andre Greipel. The stage six winner was one of a dozen riders involved in a nasty pile-up inside the final three kilometres, taking the formidable Lotto Belisol train out of the equation.
After his run-in with Argos-Shimano’s Tom Veelers on Tuesday and his unsavoury experience involving a disgruntled fan and a bottle of urine during Wednesday’s time trial at Mont-Saint-Michel, Cavendish looked certain to have put his recent travails behind him with a second win of the race.
But Kittel powered through from behind to secure his hat-trick and Germany’s fifth stage of the race. Following Kittel’s victory on Tuesday and Tony Martin’s ITT success on Wednesday, this is the first time in the history of the Tour that Germany has won three consecutive stages.
“I’m speechless. I feel really good. I would like to dedicate this win to my team – especially Tom Veelers, who had to fight today just to finish,” said 25-year-old Kittel.
“They say good things happen in threes and that has happened for me today.”
Cavendish, who won stage five in Marseille in the opening week of the race, was stoic and gracious in defeat after his latest setback.
“He [Kittel] was just a bit too quick for me,” he told reporters after the stage. “My team did such a good job again but I just didn’t have the legs.”
Britain’s Froome narrowly missed coming down in the large pile-up and then had a number of dicey moments in the last two kilometres as he rode near the front in a bid to avoid any spills.
“It’s always like that in the final before a sprint,” said the 28-year-old race leader. “Today there were some crashes and that’s always a scare. It’s hard because there are crashes all over the place.”
Froome’s Norwegian team-mate Edvald Boasson Hagen was one of the riders who fell heavily in the large pile-up towards the finish. Although Boasson Hagen crossed the line holding his left shoulder, Team Sky manager David Brailsford told the press that he had not broken his collarbone.
Other than the feisty finale, stage 12 was a rather monotonous affair whose main highlights came more from the glorious chateaux of the Loire valley than any action on two wheels.
A break of five rode clear of the peloton after the Italian Francesco Gavazzi (Astana) attacked three kilometres from the start at Fougeres.
Gavazzi was joined by follow Italian Manuele Mori (Lampre-Merida), Spaniard Juan Antonion Flecha (Vacansoleil-DCM) and French duo Romain Sicard (Euskaltel) and Anthony Delaplace (Sojasun), the five fugitives building up a maximum lead of nine minutes under bright blue sky.
This advantage was whittled down to just three minutes by the time the leaders passed through the intermediate sprint 50km from the finish. The sprint at Savigne-sur-Lathan offered a rare moment of action in the peloton, with green jersey Sagan shaking his fist at Belgian Kris Boeckmans after the Vacansoleil-DCM rider appeared to box in Cannondale’s Sagan beside the road barriers.
Sagan nevertheless finished in the wheels of Cavendish and Greipel to consolidate his green jersey points haul. There was no let-up for the teams of the sprinters who, once the intermediate gallop was done, re-grouped in pursuit of the escapees.
Flecha was the last of the break to be caught by the pack, the Spanish veteran reeled in with 6km remaining after a gutsy attempt to stave off the inevitable.
Canadian veteran Svein Tuft crashed on the front of the peloton after the Orica-GreenEdge veteran entered a roundabout 4km from the finish with too much speed.
Omega Pharma-Quick Step came to the front alongside Argos-Shimano – and Lotto Belisol were just forming their train when the pile-up happened 2km from the finish, effectively ending their chances of guiding the German national champion Greipel to his own second win.
By not placing in the final sprint, Greipel lost ground in the battle for the green jersey, with Slovakia’s Sagan now leading Cavendish by 96 points, and the German dropping to third place a further 16 points in arrears.
There was no change in the overall standings, with Froome retaining his 3:25 lead over Spaniard Alejandro Valverde (Movistar). Dutchman Bauke Mollema (Belkin) is third at 3:37 and Spain’s Alberto Contador (Saxo-Tinkoff) is fourth at 3:54.
The Tour continues on Friday with the flat 173km stage 13 from Tours to Saint-Amand-Montrond – a chance for Cavendish to get a belated second win, or perhaps for Kittel to take a historic fourth victory.