The company said in a statement that Thompson would be replaced on an interim basis by Ross Levinsohn, the company head of global media. The company also said it had named Fred Amoroso as chairman of the board of directors, replacing Roy Bostock.
Thompson, who took over as head of the struggling company less than six months ago, claimed he received degrees in accounting and computer science from Stonehill College near Boston, but Yahoo's largest outside investor revealed earlier this month that the accounting degree was the only one he earned.
Yahoo admitted Thompson did not receive a computer science degree, but termed it an "inadvertent error." That did not halt the controversy stemming from the revelation, however, and Thompson's attempts at damage control -- two apologies to Yahoo staff and claims that the error resulted from a mistake by an executive search firm that recruited him to his former job at PayPal -- did little to calm calls for his job.
The Wall Street Journal's AllThingsD blog first reported that Thompson would be leaving Yahoo.
AllThingsD reported that Levinsohn was one of two Yahoo officials that the investor who told the world of Thompson's false degree claim -- Daniel Loeb, head of Third Point, which owns 5.8 percent of the company -- mentioned as possible replacements in follow-up letters to the company demanding Thompson's dismissal.
Yahoo's board on Sunday also agreed to a deal to settle a proxy contest with Third Point, which has been publicly and loudly agitating for changes at the company since former CEO Carol Bartz was dismissed in September.
Yahoo said that Loeb and Third Point nominees Harry J. Wilson, and Michael J. Wolf would join the Yahoo board on May 16. It said Bostock, Thompson and board members Patti Hart, VJ Joshi, Arthur Kern and Gary Wilson, who were not standing for re-election, would leave immediately.
"We are confident this board will benefit from shareholder representation, and we are committed to working with new leadership to unlock Yahoo's significant potential and value," Loeb said in the statement released by Yahoo.
Thompson had been CEO of Yahoo for less than six months, officially taking the helm in January after being named the replacement for Bartz late in 2011. Previously, he was president of the San Jose-based eBay (EBAY) subsidiary PayPal.
Contact Jeremy C. Owens at 408-920-5876; follow him at Twitter.com/mercbizbreak.