The Manx sprinter completed five stages of the seven-stage race but decided not to start stage 6.
He will now travel to the UK for the Commonwealth Games road race, which takes place on Saturday and where he'll have the rare opportunity to represent the Isle of Man.
"I’m sorry to leave the boys and the race, but at the same time I’m looking forward to racing for the Isle of Man at this great event, and I want to thank the team for their support," Cavendish said in a statement from his team.
Cavendish usually represents Great Britain in international competition but the Commonwealth Games see the nations and Crown Dependancies of the United Kingdom split up into competing entities.
He will race against the likes of Geraint Thomas (Wales) and Fred Wright (England) in Sunday's road race, which takes place in Warwick.
The route takes in 10 laps of a 16km circuit around the town, with no significant climbs and just 130 metres of elevation on each lap. Cavendish therefore has every chance of the gold medal but a bunch sprint is still far from a foregone conclusion in a race that's sure to be unruly in the absence of traditional team units.
Cavendish had returned to action at the Tour de Pologne on Saturday for the first time since winning the British road race title at the end of June, having missed out on selection for the Tour de France.
The 37-year-old was a flag-bearer for the Isle of Man at the opening ceremony in Birmingham last Thursday before a hasty flight to Poland for the WorldTour stage race. Cavendish did not enjoy any success during his time at the race, placing 8th and 10th in the opening sprints.
Cavendish's schedule for the second half of the season has yet to be confirmed. He is out of contract and set to leave QuickStep at the end of the year, with negotiations ongoing with a number of teams as he looks to race on for two more years and try to break the Tour de France stage win record.
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Deputy Editor - Europe. Patrick is an NCTJ-trained journalist who has seven years’ experience covering professional cycling. He has a modern languages degree from Durham University and has been able to put it to some use in what is a multi-lingual sport, with a particular focus on French and Spanish-speaking riders. After joining Cyclingnews as a staff writer on the back of work experience, Patrick became Features Editor in 2018 and oversaw significant growth in the site’s long-form and in-depth output. Since 2021 he has been Deputy Editor - Europe, taking more responsibility for the site’s content as a whole, while still writing and - despite a pandemic-induced hiatus - travelling to races around the world. Away from cycling, Patrick spends most of his time playing or watching other forms of sport - football, tennis, trail running, darts, to name a few, but he draws the line at rugby.