The Dutchwoman had suffered a horrific accident in the Rio Olympics road race that left her with three spinal fractures
Colombian Chaves slips 36 seconds behind Froome in the general classification
The 30-year-old won a sprint bronze for Australia at the 2012 Olympics in London
The Spaniard is one of only six men with titles in all three grand tours and he won most of them in swashbuckling fashion
The Spaniard was Chris Froome's right-hand man in the mountains and looked strong on the Izoard climb, launching an attack which ultimately came to nothing.
The Briton suffered a few hiccups, but was always in control over the three-week race
The Team Sky rider extended his lead to 54 seconds going into Sunday's 21st stage, largely a processional ride to Paris.
Froome kept hold of the race leader's yellow jersey ahead of Saturday's decisive time-trial in Marseille
Froome finished fourth, giving up four bonus seconds to Romain Bardet but putting two more into Uran.
Meanwhile German sprint king Marcel Kittel pulled out before the halfway point of the stage after crashing in the first 20km.
Chris Froome retained the overall lead in a hectic finale to stage 16.
Dutchman Bauke Mollema won the 189.5-km stage from Laissac-Severac L'Eglise
Chris Froome retook the yellow jersey from Fabio Aru.
Another Sky rider Mikel Landa also has emerged as a potential Tour winner.
Aru takes yellow from Froome