German world time trial champion Martin, who suffered a concussion and bruises in a mass crash on the race's first stage, blasted round the flat 33-km course in 36 minutes 29 seconds to take the 11th stage.
"When the doctor said I was ok to race (after the first stage), I targeted this stage," pre-stage favourite Martin, who uses an awe-inspiring 58x11 gear in the time trials, told a news conference.
Froome, adorned in the race leader's yellow jersey, was the last man down the start ramp and was two seconds quicker than Martin at the 22-km check point.
But the Team Sky rider could not maintain the pace pedalling into a headwind over the latter part of the stage and finished 12 seconds down on Martin, with Belgian Thomas De Gendt third.
Froome was the big winner of the day, though, gaining two minutes on his nearest rival in the race standings and now leads Spain's Alejandro Valverde by 3:25.
Wednesday's result will perhaps implant a nagging doubt into the minds of his rivals that there is no use in contesting for the lead anymore - better in the mountains, better in the time trials, Froome will win the Tour.
"I'm happy with how the stage went. A time trial is always a nervous day for GC (general classification) riders so I'm happy I have extended my lead," Froome told a news conference.
The Olympic time trial bronze medallist is not taking anything for granted, even though he hammered his rivals in the first mountain stage and survived an early onslaught in the second last Sunday.
"I think that we saw last weekend that other teams are going to throw everything at us and we will try to do with the best team we've got."
Bauke Mollema of the Netherlands remains third overall 3:37 back with twice Tour champion Alberto Contador fourth at 3:54 after riding a decent, yet unimpressive time trial.
"It's a big (time) difference. Things are getting complicated but, no, the Tour is not lost. No one has won the Tour yet," Contador told reporters.
Valverde, instead, seemed to be content with his second place overall.
"Two minutes (the time he lost to Froome) is a lot but you've got to look at the other riders who are fighting for a podium finish," the Movistar rider said.
"I was with the bests, I'm happy."
Cadel Evans's performance on the stage, 21st 2:30 behind Martin, confirmed the 2011 champion was past his prime.
"I did not feel bad, but not great either," the Australian, now 14th overall almost seven minutes off the pace, told reporters.
Andy Schleck of Luxembourg will effectively have to focus on a stage win as his slim hopes of featuring somewhere in the top five evaporated when he finished an embarrassing 123rd, 4:44 off the pace.
With some of his rivals, like Valverde, apparently already gunning for no more than a podium finish, Froome could use a defensive strategy in the Alps, starting with Sunday's stage up the Mont Ventoux, with the help of his team.
"Richie (Porte) slipped back from second place in GC but he showed today that he is not out of this race," said Froome, referring to the Australian's fourth place in the stage.
"I expect him to be there in the mountains with Pete Kennaugh.
"Alejandro Valverde is the rider whom I have to take care of the most," he added.
"But I think there are other guys that we will have to mark for the next week."
There was little to smile about for Mark Cavendish, however, as the Briton had urine thrown at him on his way to the Mont Saint Michel - yet another jaw-dropping backdrop for the 100th edition of the Tour.
"Mark is one of the big characters in the sport, some people love him, others hate him, but to do this is very sad," said Froome. "It ruins the whole atmosphere. It leave a bad taste in your mouth. A bad taste in Mark's mouth."
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