Riders and officials, with German champion Andre Greipel in front of the peloton, observed a minute's silence in tribute to the victims of Friday's mass shooting in Munich before the start of the stage.
Froome, in the yellow jersey, was joined by Yates in the white jersey as best young rider, Slovak Peter Sagan in the green points top and Poland's Rafal Majka in the polka dot king of the mountains jersey.
Australian Chloe Hosking had earlier won the women's La Course by Tour de France, the annual curtain-rasier to the final men's stage.
Sprinter Dan McLay surprised many with four top-10 finishes in the first week and although the Fortuneo - Vital Concept rider exhausted as the race wore on the 24-year-old made it to Paris on his Tour debut.
On the last climb to the intimidating Col de Joux Plane, an 11.6-km ascent at an average gradient of 8.5 percent, Nibali attacked to catch and drop France's Julian Alaphilippe and Colombian Jarlinson Pantano.
This year, Froome looked much more relaxed as the crowds seemingly warmed to the Kenyan-born rider.
In doing so, Froome is the first man to retain the Tour de France in over 20 years.
Froome said he will unlikely ever ride the Giro d'Italia, which Merckx also won five times, but he has unfinished business with the Vuelta a Espana.
Froome will add to his victories from 2013 and last year while 25-year-old Frenchman Romain Bardet will finish second and thus ignite hope amongst the host nation that their painful 31-year wait for a Tour victor could soon be coming to an end.
"Everyone should believe in Chris Froome.it's good to see clean guys winning", said Porte.
Chris Froome's Sky team manager Dave Brailsford vowed to come back to the Tour and win it again next year following a fourth success in five years. On Sunday, Froome is going to lock up his third victory in the race and remain dominant over the rest of the competition.
"We've tried many times and we walk away from the Tour with two stage wins, with Thomas De Gendt and myself". A win in Paris is one of the most coveted victories for sprinters.
Steve Cummings, a team-mate of Cavendish, finished more than four hours adrift of Froome but won the second Tour stage of his career with a
The image of Froome off his bike and running toward the finish up Mont Ventoux is already part of Tour de France lore.
NEXT ORDER: The 2017 Tour will start with two stages in Dusseldorf, Germany.
Cheered on by thousands of fans undeterred by the recent spate of violence across Europe, Froome celebrated his third Tour title in four years.
French hope Bryan Coquard was denied the chance to go for victory as he was held up by a late puncture, while Marcel Kittel also suffered a mechanical in the closing stages and was unable to contest the sprint.