Dutchman Olav Kooij, who won the fifth stage, took second at the end of the 161km 11th stage from Vichy to Nevers, with Belgian Milan Fretin promoted from fourth to third after his compatriot Jasper Philipsen was demoted.
At an average speed of 50.91kph, it was the fastest ever road stage in the 113 editions of the Tour.
"It means everything, it's my biggest win so far," said the 26-year-old who was second in the seventh stage to Bordeaux and last year won the Omloop Het Nieuwsblad one-day classic.
"When I came here, I knew that there are two or three guys that are faster than me, but if I'm lucky and I have a good sprint like today, then it's possible.
"Sometimes I have really good confidence, and I believe in myself, but there are many, many times where I feel super tired and it's impossible to win here."
Once again, there was a fairly disjointed sprint finish with none of the teams able to organise a sprint train to set up their fast man.
Kooij's lead-out rider Cees Bol launched off the front as the main sprinters hesitated, but Waerenskjold was the first to chase after the Dutchman.
He instantly put several bike lengths of daylight between himself and the rest, and although both Kooij and Philipsen caught him by the line, they did not have enough strength to edge past Waerenskjold.
Belgian Tim Merlier, who had won the seventh and eighth sprint stages, finished a disappointing 14th.
Eritrean Biniam Girmay finished fifth to cut Mads Pedersen's lead in the sprinters' green jersey competition to 43 points after the Dane could finish only 10th.
It was the second Tour stage victory for the Norwegian Uno-X Mobility team, which is in its first year as a World Tour outfit, after Jonas Abrahamsen succeeded once last year.
The team also held the yellow jersey for two stages this year with Torstein Traeen before he crashed out with a concussion and broken ribs.
'Strong breakaway'
Reigning champion Tadej Pogacar finished safely in the pack to retain his overall lead of more than three and a half minutes to two-time former winner Jonas Vingegaard.
He put down the rapid pace partly to the strength of the breakaway riders.
"There was a lot of chance for the breakaway to go to the finish line, and the sprint teams, they control and they need to catch them," said the 27-year-old world champion.
"Today was a strong breakaway, that's why the speed has to be high.
"Once we caught them, we slowed down immediately, and it was so funny to ride from 5km to 2km to go - we ride the slowest of all day.
"The biggest reason is also the tailwind. With the headwind will be much, much less speed.
"But when you have such a strong breakaway in front, you go fast."
A four-man breakaway had set off early into the stage which began in the ancient spa town of Vichy.
They were never allowed a longer leash than one minute and 40 seconds, and four became three when Frenchman Julian Alaphilippe, a former world champion and yellow jersey-wearer, was dropped on a short climb with around 40km left.
But Anthon Charmig, Mathis Le Berre and Nelson Oliveira collaborated well together to resist the inevitable return of the peloton.
With 10km to ride, their lead was down to just 20 seconds.
But within four kilometres, their resistance was over, and the expected sprint took centre stage.