Froome was the only rider to get within a minute of Martin, with Belgian Thomas De Gendt 1:01 behind in third.
While Martin is not a Tour challenger, others who are supposed to be slipped further behind.
Alejandro Valverde and two-time former champion Alberto Contador were two minutes or more slower than Froome, and 2010 champ Andy Schleck and 2011 champ Cadel Evans lost massive time.
Valverde is still in second place overall but is 3:25 back.
Contador looked stern-faced and tense when he prepared to start. He's now almost four minutes behind Froome.
The Spaniard finished in 15th place, 2:15 behind Martin; Evans was 2:30 slower and Schleck finished 4:44 behind Martin.
"No one's won the Tour de France yet and no one's lost it. We have to get to Paris yet," Contador said. "It's true that Chris Froome is in impressive form and is a great climber, but there are still many stages left."
Martin was lucky to still be in the race after losing consciousness on his team bus after his crash in the opening stage. It was so bad that his left lung was bruised and layers of skin were shredded off his back, preventing him from sleeping properly for several nights.
"It's pretty much OK. There are still some deeper wounds that are left to heal, but it's not that painful anymore like directly after the crash," Martin said. "(Today) the feeling was good. I was just focused on the race. It was more or less like every time trial."
Martin won the penultimate stage of the 2011 Tour, an undulating time trail in Grenoble. He also finished second behind Bradley Wiggins in the time trial at the Olympic Games last year in London.
The ride Wednesday started in Avranches, whose website dates the town's origins to Celts in the 9th century B.C. It ended at the breathtaking island citadel of Mont-Saint-Michel, a World Heritage site because of the Gothic-style Benedictine abbey erected between the 11th and 16th centuries.
However, riding at an average speed of 34 mph in humid conditions, there was little time for Martin to take in the sights.
Mark Cavendish had an eventful day but for the wrong reasons.
Cavendish's team said it believes someone threw urine at the British rider.
"Yes, that's true I think. I was behind him. I didn't see it, but I think it's true," the team press officer Alessandro Tegner said.
Tegner said the liquid smelled like urine and it was "all over him." He added Cavendish talked about it after the time trial.
1. C. Froome Leader
2. A. Valverde +3:25
3. B. Mollema +3:37
4. A. Contador +3:54
5. R. Kreuziger +3:57
Tour de France
O Thursday, 6 a.m.
TV • NBCSN