He had been aiming to set a new all-time record of 35 wins but he just missed out in the final leg from Chatou to the Champs-Elysees in Paris as he got squeezed out on the run to the finish line.
He banged his handlebar in frustration as he came third in the mass sprint which was won by Belgian Wout van Aert, with Jasper Philipsen, also of Belgium, second.
Slovenian Tadej Pogacar claimed the yellow jersey with his second successive Tour title after Sunday’s 21st and final stage.
The UAE Emirates rider also won the white jersey for the best Under-25 rider and the polka-dot jersey for the mountains classification after a dominant performance throughout.
Cavendish, who last won the green jersey in 2011, on 9 July equalled Merckx’s record – which had stood since 1975.
The Manx rider crossed the finish line in Carcassonne to win stage 13. He also won stages four, six and 10 on the 2021 tour.
It capped a remarkable turnabout in fortune for the 36-year-old rider, who had hinted last year that his career may be over after a run of poor form and illness.
In October, Cavendish suggested he may retire from cycling at the conclusion of the Gent-Wevelgem race in Belgium.
He said that race could be his final one, but signed for Deceuninck-Quick Step for the 2021 season and was drafted on to the team’s Tour de France roster last month after an injury to his teammate and fellow sprinter Sam Bennett.
On Pogacar’s success, five-time Tour champion Merckx said: “I see him as the new Cannibal.”
Merckx, who won his first Tour in 1969 at the age of 23, earned that nickname due to his insatiable appetite for victory.
He added: “He is extremely strong. I see him winning several editions of the Tour in the years to come. If nothing happens to him, he can certainly win the Tour de France more than five times.”
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