Yahoo shares are down more than 3% this morning after the company said that it has bought back most of the shares owned by Third Point’s Daniel Loeb — leading him and colleagues Harry Wilson and Michael Wolf to resign from the board at the end of this month. ”Since our Board’s rigorous search led us to hire Marissa Mayer as CEO, Yahoo!’s stock price has nearly doubled, delivering significant value for shareholders,” Loeb says. “I’m confident that with Marissa at the helm and her team’s focus on innovation and engaging users, Yahoo! has a bright future.” The agreement to buy 40M of Loeb’s shares, at $29.11 apiece, will bring his stake in the company below 2% — and will count toward the company’s plan to repurchase $1.9B of its stock. Loeb is an investor in Variety with Deadline’s parent company PMC.

The sale makes sense for Loeb, the billionaire founder of hedge fund Third Point. He’s a value investor who likes to engage in deep research and then bet on relatively boring companies and assets that others overlook. Few would consider Yahoo undervalued after its stock appreciated 77% in the last 12 months. And the company is far from overlooked with former Google exec Mayer at the helm. The sale gives Third Point cash to devote elsewhere — possibly including Sony where Loeb is urging the company to issue stock in its movie, TV and music assets. (He wants Sony to hang on to about 80% and let the public trade the remaining 20%.) Meanwhile, Third Point remains a major shareholder in Yahoo.

But Yahoo shareholders may fear that once Loeb and his colleagues leave the board, the company may use the proceeds from the interest it sold in Alibaba to buy assets — like it just did with its $1.1B deal for Tumblr — says Barclay’s Capital’s Anthony DiClemente.

Here’s the release:

SUNNYVALE, Calif.– Yahoo! Inc. (NASDAQ: YHOO) today announced that it has entered into an agreement to repurchase 40 million shares of Yahoo! common stock beneficially owned by Third Point LLC (“Third Point”), at a purchase price of $29.11 per share. The purchase price equals the closing price of Yahoo! common stock on July 19, 2013.

Following the repurchase, Third Point will beneficially own approximately 20 million shares, representing less than 2 percent of Yahoo!’s outstanding common stock. In accordance with the Board’s settlement agreement announced on May 13, 2012, each of the directors originally nominated by Third Point — Daniel S. Loeb, Harry J. Wilson, and Michael J. Wolf — have submitted their resignations from Yahoo!’s board of directors, effective July 31, 2013. The Board will then comprise seven members. Max Levchin, who was appointed as a director upon mutual agreement between Third Point and the Board, will remain on the Board. The remaining directors are committed to revisiting the Board’s size and composition.

“Daniel Loeb had the vision to see Yahoo for its immense potential – the potential to return to greatness as a company and the potential to deliver significant shareholder value,” said Yahoo! CEO Marissa Mayer. “On behalf of the Board and our entire team, I’d like to take this opportunity to personally thank Dan, Michael, and Harry for the tremendous opportunities they created here at Yahoo!. They have been incredibly supportive as we have built our executive staff and developed our strategy, and they have helped position Yahoo! for future success. While there’s still a lot of work ahead, they’ve given us a great foundation.”

“Harry, Michael and I are pleased to have played key roles in Yahoo’s resurgence since we joined the Board last spring,” said Third Point CEO Daniel S. Loeb. “Since our Board’s rigorous search led us to hire Marissa Mayer as CEO, Yahoo!’s stock price has nearly doubled, delivering significant value for shareholders. I’m confident that with Marissa at the helm and her team’s focus on innovation and engaging users, Yahoo! has a bright future.”

Yahoo! previously announced a plan to purchase an additional $1.9 billion of Yahoo! common stock; the new repurchase agreement becomes part of that plan. Upon completion of this repurchase, approximately $700 million will remain under the $5 billion buyback authorization announced last year, on which the Company plans to continue to execute. Yahoo! expects to fund the transaction primarily with cash, and the transaction is accretive to earnings per share (EPS).