The German, who won the first stage and wore the yellow jersey in both 2013 and 2014, sprinted ahead of Frenchman Bryan Coquard (Direct Energie) and Peter Sagan (Tinkoff) for the victory.
It was his first Tour win since the final stage of the 2014 race, where he left with four wins and after a 2015 season affected by sickness.
This winter, Kittel switched from Giant-Alpecin to lead Etixx after Mark Cavendish departed to join Dimension Data.
"I don't know if you can explain emotions, they just come out," Kittel said after the stage.
"For me, the victory means a lot because I know how hard I worked to get here after being sick last year so many times and missing out on the Tour and also so many race days.
"It was a very difficult moment in my career. I actively tried to take action to make changes and improvements for myself to be at this level to win stages in the Tour. To see it now working so well, though the first part of the Tour was not as we wanted, is a huge achievement. I live for my sport, although the critics said something else last year."
The critics began to write when he returned to Europe sick after Australia’s Tour Down Under. He had to cancel race participations, abandon others midway through and re-start after multiple rest periods.
Though he said that he felt ready for the 2015 Tour, Giant-Alpecin overlooked him. That winter, Etixx called him after its star sprinter left.
Watch highlights of Marcel Kittel's Tour de France stage win
He appeared ready to win stage one as he has done twice before and pull on the yellow jersey when the race began in Normandy on Saturday.
Kittel had already won two stages in the Giro d'Italia in May and wore the pink jersey, plus tested himself against the other top sprinters on other occasions this spring and came out on top. His team, however, failed to click and Cavendish seized his chance.
"We had a meeting [on Monday]. The difference is that we could make the switch in our heads to stay calm and really follow our plan," Kittel said.
"If you look at our team, on paper we are super strong. We have really strong pilots like Iljo Keisse and Tony Martin, who are good at leading out. We also have guys who are doing their first Tour, that means they have to get used to it.
"In a stage in the Tour, the sprint starts 20 kilometres before the finish line, no other race is like that. I had to calm them down and get them used to what happens here."
Kittel now counts nine stages wins, one from this year and four each from 2013 and 2014. More could come after the race tackles its first climbing stage on Wednesday through the Massif Central.
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