By Chelsey Dulaney And Jeffrey A. Trachtenberg 

Microsoft Corp.'s flirtation with Barnes & Noble Inc. has ended, clearing the way for the nation's largest bookstore chain to get on with its plans to split itself into two separate public companies.

Barnes & Noble said Thursday that it is buying out Microsoft's 16.8% stake in Nook Media LLC for about $125 million in cash and stock.

Microsoft agreed in 2012 to invest $605 million in Barnes & Noble's Nook digital device and e-book business and its college bookstore group. The investment included a $300 million equity stake plus additional investments through 2017.

In return, Barnes & Noble committed to creating e-reading apps for new computers, phone and tablets powered by Microsoft's Windows software. Wall Street analysts and investors wondered whether Microsoft would eventually make a larger commitment to Barnes & Noble, but that never materialized.

In a statement Thursday, Microsoft said, "As the respective business strategies of each company evolved, we mutually agreed that it made sense to terminate the agreement."

Barnes and Noble said its separation into two companies--one consisting of 658 consumer stores and BarnesandNoble.com, and the other made up of college bookstores and the Nook digital business--will happen at the end of August 2015, instead of the earlier target of March.

"Sorting out Microsoft is an important step," said John Tinker, an analyst with Maxim Group. He said buying out the software giant gives Barnes & Noble "more options regarding the future of the Nook business and the entire company."

Pearson PLC continues to own a 5% stake in Nook Media.

The disclosure of the Microsoft transaction came as Barnes & Noble reported results for the November quarter, posting a profit of $12.3 million, or 12 cents a share, down from $13.2 million, or 15 cents a share, a year ago. Revenue fell 2.7% to $1.69 billion.

Mr. Tinker said the company's revenue was "solid" but earnings before interest, taxes, depreciation and amortization were "lighter than expected." Barnes & Noble shares were down 13% in morning trading.

The Nook segment's revenue fell 41% to $63.9 million, while digital content sales fell 21% to $45.2 million.

Since the initial deal was struck with Microsoft, circumstances for both companies have changed. Barnes & Noble slowed work on its e-reading devices and tablets as its sales slumped and laid off much of the workforce devoted to its Nook devices.

In June, it signed deal to sell color tablets made by Samsung Electronics Co. co-branded with the book chain's Nook label. The deal was seen fulfilling Barnes & Noble's previously stated plan to reduce its heavy investment in the Nook, allowing the retailer to focus more on its stores and college business.

Meanwhile, Microsoft, which has its own Windows tablets and smartphones, shifted its consumer-device strategy following sales hiccups.

Barnes & Noble has sought to inject excitement into its stores to combat the tepid store traffic that has plagued much of the retail industry because of online shopping. The retailer has gotten more creative with how it organizes its titles, added new displays and toys, and introduced big-ticket gifts like beer kits and turntables.

Mr. Tinker said it was a positive sign that the retail store group showed core comparable-store growth of 0.5%, a figure that excludes the sale of Nook digital products.

"What that tells you is that the book business has stabilized and that the repositioning of the stores with more focus on gifts and educational toys and games is working," he said.

Still, revenue at the retailer's consumer bookstores fell 3.6% to $888 million, primarily because of declining sales of Nook products. Comparable-store sales were down 1.5%.

-Shira Ovide contributed to this article.

Write to Chelsey Dulaney at chelsey.dulaney@wsj.com

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