Three team mates of defending champion Jonas Vingegaard crashed when Sepp Kuss hit the spectator's arm and lost his balance.
German Lennard Kamna and Bora-Hansgrohe team mate and compatriot Maximilian Schachmann were second and third respectively.
The 22-year-old Bernal, the youngest rider to win the race in 110 years, gave Team Ineos --formerly Team Sky -- their seventh title in the last eight editions.
Caleb Ewan claimed his second victory in this year's Tour de France when he prevailed in a tightly contested sprint to win the 11th stage,
Briton Adam Yates retained the overall leader's yellow jersey after staying tucked in the main peloton, which crossed the line with a deficit of 2:53.
The Slovenian played it safe on the last climb of the day but it was enough for him to move to the top of the standings in a ninth stage won by Tour debutant Pogacar.
The World No 1 sustained the pace in the climbs up to the Col de Vars and the Col d'Izoard, both culminating at more than 2,000 metres, but then lost ground when his compatriot Thibaut Pinot accelerated to rein in defending champion Geraint Thomas.
Michal Kwiatkowski, the unsung hero of Team Sky/Ineos during their dominant years, claimed his maiden Tour de France victory
Roglic leads Pogacar by 40 seconds and Colombian Rigoberto Uran by 1:34 as the race is turning into an all-Slovenian affair following Bernal's disappearance.
Norway's Kristoff outsprinted Danish world champion Mads Pedersen after 156 km around Nice.
Tadej Pogacar became the first Slovenian to win the Tour de France after he retained the yellow jersey in the 21st stage on Sunday, a day after he pulled off a major coup to take the overall lead.
All team members, riders and staff had until 1100 GMT on Monday, the Tour's first rest day, to take a test in the mobile laboratory provided by organisers.
Stage eight winner Nans Peters had long crossed the line when fellow Frenchman Thibaut Pinot's ordeal ended after the Groupama-FDJ rider, highly fancied to become the first local winner of the race in 35 years, had been dropped in the second ascent of the 141-km trek through the Pyrenees.
Formula One champion Lewis Hamilton and Barcelona forward Lionel Messi were declared joint winners of the Laureus World Sportsman of the Year Award in Berlin on Monday, with the voting tied for the first time in the awards' 20-year history. Mercedes driver Hamilton won his sixth world championship in 2019, with 11 race wins and 17 podium finishes, while Messi was crowned the world's best player for a record sixth time when he won the Ballon d'Or. American gymnast Simone Biles, who became the most decorated gymnast in world championship history when she won her 25th medal last year, won her third Sportswoman of the Year gong after winning the award in 2017 and 2019.
Rafael Nadal is in contention for the 'World Sportsman of the Year' award alongside six-time Formula 1 World champion Lewis Hamilton, six-time World MotoGP champion Marc Mrquez and six-time FIFA World Footballer of the Year Lionel Messi.
Makes us wonder how these cyclists don't fall short of breath as they pedal to the finish line. Here's a glimpse of the tricky but beautiful terrain that outlines the Tour de France...
Geraint Thomas tightened Team Sky's grip on the Tour de France when he handed the British outfit their sixth title in seven years on Sunday and there is no sign that their domination will end anytime soon.
Summary of sports events and persons who made news on Thursday.
A summary of sports events and persons who made news on Tuesday
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