Froome lost nearly a minute to his team-mate on the opening stage of the Tour when he crashed in a field five kilometres from the finish, and gave up another five seconds when he was gapped slightly on the Mur-de-Bretagne on Thursday.
As Froome lost six seconds on the steep climb to the Mur de Bretagne finish, Thomas gained two seconds on stage six and is now second in the general classification, just three seconds behind Porte's BMC teammate Greg Van Avermaet.
"There's no reason I can't look at it [the Mûr de Bretagne], even though I'm contending for GC [the general classification]", Martin said earlier this week.
"So I set off, kept my head down, kept going and my legs felt good". I wanted to give it some time to see if the good legs would get there.
"I was following quite good wheels but it was choppy". It's fantastic, I'm really grateful for myself and for my team.
Outside the AG2R team bus at the Tour de France starting line in Lorient on Wednesday there stood just seven warm-up bikes, with Axel Domont no longer needing his after a 70km per hour fall on the previous day's stage.
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Defending champion Chris Froome crossed eight seconds after Martin in 18th.
There was further fallout too from Tom Dumoulin's time penalty, imposed after Thursday's finish to Mûr-de-Bretagne, when Froome's rival slipstreamed his team vehicle after suffering a broken wheel five kilometres from the finish. "I don't know if he did it on goal but he dropped a lot of people", Sagan said.
Belgian Greg Van Avermaet retained the leader's yellow jersey ahead of Saturday's eighth stage and said he hope to go to the mountains with it next week after what he described as a relaxing day.
"The Mur de Bretagne is much harder than this", said Van Avermaet, who would not rule Sagan out of contention for the sixth stage.
Dumoulin, the time trial world champion and 2017 Giro d'Italia victor, was slowed by a tire puncture at the foot of the final ascent and lost 53 seconds.
The 231km stage from Fougeres to Chartres saw multiple breakaway attempts, but on a flat route with occasional crosswinds, none seemed likely to stick - not least because the majority were undertaken by lone riders.