The San Jose, Calif., company, which is sparring with activist investor Carl Icahn over board seats and its future direction, also gave Donahoe, 53, and other executives a lower-than-targeted incentive payment earlier this year. It noted that eBay missed financial targets last year, according to a regulatory filing.
EBay's compensation committee "concluded that while Mr. Donahoe continued to perform well against many ... goals, the (company's) financial performance for 2013 and positioning relative to its competitors at the start of 2014 did not fully meet expectations," it said in a proxy statement filed Monday.
EBay's earnings rose 9 percent and revenue climbed 14 percent last year, as the company closed out 2013 with a strong holiday season. Its stock also rose 8 percent to end 2013 at $54.86, but the Standard & Poor's 500 index soared more than 29 percent last year.
EBay is fighting a push by Icahn to split the company in two by spinning off its PayPal payment arm, which is growing more quickly than the rest of the company. The investor also has nominated a pair of directors for eBay's board and complained about Donahoe's performance.
Icahn contends eBay sold video-chat site Skype prematurely, a move that cost shareholders $4 billion.
EBay is urging shareholders to support its directors, and it strongly believes PayPal should stay part of the company. No date has been set yet for the annual meeting at which shareholders will vote on the board and other issues.
For 2013, Donahoe received compensation totaling $13.8 million. That included a salary of $993,269 and a performance-based bonus of $1.6 million, which was down 43 percent. The company awarded this bonus earlier this year based on its 2013 performance.
Donahoe also received stock and option awards totaling about $11.1 million in 2013. That's less than half of what he received in 2012, when eBay gave the executive a one-time, $14.9 million grant as part of the company's performance-based incentive plan. Donahoe also received more than $20 million in stock and option awards in 2008, the year he became CEO.
Excluding the stock and option awards, Donahoe's compensation for 2013 fell 30 percent compared with 2012.
The Associated Press formula calculates an executive's total compensation during the last fiscal year by adding salary, bonuses, perks, and the estimated value of stock and stock options awarded during the year. The AP formula does not count changes in the present value of pension benefits.
EBay shares climbed 33 cents to $58.55 in midday trading Tuesday.