Arnaud Demare of FDJ holds it for now, but Kittel is closing in after his second win of the Tour.
The seventh stage of the Tour de France burst into life at the finish on Friday as Marcel Kittel claimed his third victory in this year's edition, pipping Edvald Boasson Hagen to the line in the final sprint.
"First of all I m going to enjoy this moment because I had a great spring and won the Italian title but before that I had a tough time", said Aru, who had to pull out of May s Giro due to injury.
Tasmanian BMC Racing rider Richie Porte retained fifth position after stage six of the Tour de France.
In the meantime, the top sprinters will have two days to lick their wounds and try to conjure up a way to stop Kittel. Kittel said before the Tour he could only take green if Sagan was eliminated, and now he has his opportunity.
While Sagan was castigated for causing Cavendish to crash, Demare got away largely scott free from criticism for a violent swerve that cut across the path of his copatriot Nacer Bouhanni in Tuesday's fourth stage, which he won.
He was repeatedly asked after his win about their absence.
Porte moved up to fifth at 39sec, with Quintana ninth at 54sec.
"To me, it's a little bit pointless", Brit Daniel McLay (Fortuneo-Vital Concept) said.
On a sweltering day in which the mercury pushed the high 30s, a breakaway of three riders - Frenchman Perrig Quemeneur (Direct Energie), Norway's Vegard Stake Laengen (UAE Team Emirates) and Belgian Frederik Backaert (Wanty-Groupe Gobert) - rode clear of the peloton in the opening kilometre.
"It was such a long day".
"If they just have true point to point stages, where the stage starts where it left off the evening before, then they don't have opportunities to make it shorter", Lotto-Soudal sports director Frederik Willems said.
"As we say, there is nothing to gain but so much to lose".
"When there's a photo finish you always have doubts and there again it really was so close".
Kittel clocked slightly more than five hours over the mostly flat 213.5-kilometer (132-mile) leg from Troyes in champagne country to Nuits-Saint-Georges in the heart of the Burgundy winemaking region. "They sure are long days".