Shares of Sears were down more than 7 percent on the news.
Berkowitz, who serves as the chief investment manager of Fairholme Capital Management, joined Sears' board in February of last year. His relationship with the retailer's chief executive, Eddie Lampert, dates back much further, though.
"On behalf of the board of directors and management, I want to thank Bruce for his long-term commitment and investment in Sears Holdings," Lampert said in prepared remarks. "His leadership, guidance and counsel as a board member have been invaluable to our company."
Lampert also serves as the chairman of Sears' board.
"I wish the company and its associates all the best as Sears Holdings continues to execute on its strategic priorities," Berkowitz said in a statement.
Berkowitz took his first stake in the department store retailer in late August 2005, through his Fairholme Fund, filings show. The fund, managed by Berkowitz, peaked in 2011 and has since tumbled as Sears shares have fallen.
Nonetheless, Berkowitz hasn't given up on the company. Fairholme remains one of the top investors in Sears, aside from Lampert's hedge fund, ESL Investments.
"Life is not smooth," Berkowitz said about Fairholme Fund's returns in an interview with The Wall Street Journal in June.
Berkowitz also has invested in Seritage Growth Properties, a real estate investment trust that spun off from Sears two years ago. Among the retail REITs, Seritage is one of the most heavily shorted stocks on the market today.
In 2010, fund-research firm Morningstar named Berkowitz U.S. stock fund manager of the decade. But his credibility in picking investments has since declined as his fund's performance has waned.
"Mr. Lampert and Mr. Berkowitz have a long-standing partnership and continue to have great respect for each other," a Sears spokesman told CNBC in a statement. "They both expressed their appreciation for the time they spent together serving on Sears' board of directors."
With Monday's declines, Sears' stock is down more than 33 percent this year.