The German sprinter looked to be struggling as the leaders roared towards the finish in Troyes but ended up winning the sprint by a bike's length for his 11th Tour stage victory.
The Quick-Step Floors rider, who also won the second stage, crossed the line in front of Frenchman Arnaud Demare and fierce rival Andre Greipel.
Kittel and Greipel are now tied for Tour stage wins, but Kittel has been looking in ominous form on this Tour and he will be the favourite again for Friday's seventh stage that takes the peloton over 213.5 km through the vineyards from Troyes to Nuits Saint-Georges.
"I'm proud of my team, they did a great job because it was a very different finish to Liege," Kittel said after the 216km ride from Vesoul.
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"The last kilometre was a little bit freestyle, but I had a good wheel to follow in Demare, and then I had to go on my own from 250m. I feel good at the moment, and for sure I have (the green jersey) in my focus."
In the points classification, Kittel trails Demare (FDJ) by 27 points, after Peter Sagan, who was targeting a sixth consecutive green jersey, was kicked out of the race for sending Mark Cavendish crashing in the finale of the fourth stage.
Sagan's team, Bora-Hansgrohe, appealed before the Court of Arbitration for Sport (CAS) but sport's highest court rejected their request of having the world champion reinstated.
Race leader Chris Froome finished safely in the pack to retain the yellow jersey, 12 seconds ahead of his Sky team mate Geraint Thomas with Italian Fabio Aru (Astana).
"This was one of my most relaxed days on the Tour de France," said Froome.
The GC (general classification) contenders will return to proper action on Sunday for a stage featuring three out-of-category climbs and a dangerous descent into Chambery.
(Editing by Catherine Evans)
