The changes mark the end of the five years of dramatic growth of the Vancouver-based company with Wilson and outgoing CEO Christine Day at the helm.
"Christine Day's five or so years at Lululemon can only be described as wildly successful and her presence, talents, and motivational skills will be missed," RBC Capital Markets analyst Howard Tubin wrote in a note to clients.
"In addition, while Mr. Wilson's most recent role at the company was non-operating, we believe he was still involved on the creative side of the business and still had/had close relationships with design and merchant teams. His creative energies will be missed as well."
Day has overseen the company's expansion beyond yoga clothes to all manner of workout gear, more than tripling the company's share value since she took over as chief executive in 2008.
Lululemon has also doubled its number of stores compared with 2008 with 226 locations in North America and Australia at the end of its most recent quarter.
However, Lululemon has struggled this year with its first major stumble when it pulled its black Luon pants from store shelves after customer complaints that the pants were too sheer. The recall was followed by the abrupt departure of chief product officer Sheree Waterson.
The company blamed the problems on a style change and production issues and moved to fix the problems, but later new complaints about the quality and durability of their pricey workout gear.
In an interview last month, Wilson touched off a flurry of criticism by suggesting to Bloomberg TV that production issues may not be the only issue.
"Quite frankly, some women’s bodies just actually don’t work for it," he said. "It's really about the rubbing through the thighs, how much pressure is there."
Critics accused Wilson of shaming women's bodies and gathered thousands of supporters through an online petition.
Wilson later posted a video message online in which he said he was "sad for the repercussions of my actions. I'm sad for the people of Lululemon who I care so much about that have really had to face the brunt of my actions. I take responsibility for all that has occurred."
The company said Tuesday that Laurent Potdevin will take over as chief executive next month. Day is expected to remain with the company through the end of the company's financial year at the end of January to help with the transition.
Potdevin, who begin his career at luxury retailer LVMH, most recently served as president of Toms Shoes, the company that gives away a pair of new shoes to a child in need for each pair it sells. He also spent more than 15 years at Burton Snowboards, including as president and CEO from 2005 to 2010.
"One of the things I'm most passionate about and I've taken great pride over the course of my career is building global brands and Lululemon certainly has all the elements needed to continue its growth in North America and beyond," he said.
Potdevin his priority will be to immerse himself in the business.
"It is really a matter of understanding all facets of the business and collaborating with the team," he said.
The announcement of Day's replacement and the departure of Wilson come ahead of Lululemon's latest quarterly results on Thursday.
Tubin said the hiring of Potdevin and the recent addition of Tara Poseley as chief product officer removes some uncertainty at Lululemon.
"We hope the new leaders gel with the remaining senior managers and the teams who run the business on a daily basis," Tubin said.
"In addition, we'd also like to see whether Mr. Potdevin embraces the current plans in place for Lululemon or if he'll want to make his own mark on the company's strategic direction.
Wilson, who holds about 10 million shares in Lululemon or roughly a nine per cent stake in the company, according to data compiled by Thomson Reuters, will step down as chairman ahead of the company's annual meeting in June, but remain a director.
The company said the board has chosen lead director Michael Casey, a former Starbucks executive, as the next chairman.