The sprint ace has made the decision in order to fulfil his Tour de France ambitions at the Belgian outfit after spending this year's race serving as a domestique for overall winner Bradley Wiggins.
Briton Cavendish, the 2011 world champion who has 23 Tour stage wins to his name, only joined Sky a year ago.
"After a year of being part of the successes at Team Sky I've decided to leave to join Omega Pharma – Quick Step Cycling Team to pursue different goals," said Cavendish.
"It's been an incredibly fun year riding with friends I've grown up with but I'm super-excited about riding with old friends and team-mates in one of the most successful and established teams in cycling.
"I believe in the team’s project and I’m thrilled to be a part of it.”
Sky principal Dave Brailsford said Cavendish had been instrumental in the relatively new outfit's success.
"Mark has been a true champion for Team Sky this year," he said. "It's been an honour having the rainbow jersey in this team and great to work so closely with a rider I've known since he was a junior.
"He has been a real team player, making history in a Tour de France-winning team."
Wiggins was Team Sky's only priority on the Tour this year as he became the first Briton to win the world's greatest cycling race.
The 27-year-old Cavendish, who had benefited from his team mates' help the previous year to win stages, was no more than a domestique in 2012.
He still claimed three stages victories in July, including on the final day on the Champs Elysees.
"Cav won 15 races with us, including his first stage race, three Tour stages, and the fourth win in his unbeaten run on the Champs Elysees," Brailsford added.
"The sight of him winning in Paris, with the yellow jersey leading out the world champion - both in Team Sky kit - is something you'll never forget.
"We all wish Mark the very best with his future ambitions in a new team and as British rider."
The move is not related to the anti-doping ultimatum Sky sent to their riders and staff on Wednesday as Cavendish's departure had been in the works for about two months.
On Tuesday, Sky said that members of the team would be sacked unless they sign a document saying they have never doped or have never been involved in doping activities. In a statement Sky said any team members, including riders, staff and management, who refused to sign or were found to have lied would be kicked out.
Omega Pharma-Quick Step owner Zdenek Bakala hailed the 'Manxman' as a star of world sport after announcing his capture.
“Mark is one of the most outstanding riders in cycling, a true star recognised internationally for his unique style and irrefutable athletic skills,” he said.
“His extraordinary sprint (sic) have become a cycling 'must-see' that can fire up crowds the world over. In addition to raising the technical bar for the team, his arrival will broaden our international profile and team image.
"Mark is an important player in the gradual growing process in which the team has invested. This year our hard work and commitment have already taken us among the best teams in the world in the UCI rankings and carried us to victory in the Team Time Trial World Championships.”
- Team Sky