Revenue in stores open at least one year continued to slide, down 4.3 percent for the quarter. The measure is an important gauge of a retailer's financial health because it excludes results from stores that open or close during the period.
Sales growth in mobile phones, appliances and tablets and e-readers was offset by weakness in notebook computers, video games, digital cameras and TVs.
Shares fell $1.79, or 13 percent, to close at $11.96 after falling as low as $11.74 earlier in the session. That is the lowest since December 2000.
The quarter had some quarter-specific issues that hampered results, Joly said, including customers delaying purchases ahead of new launches like the new Windows 8 operating system and several new smartphones and tablets.
In addition, the company faced higher costs for training employees and executive transition expenses.
"We do not believe that the rate of decline that Best Buy experienced in the third quarter can be extrapolated in any way," he said in a call with analysts.
Best Buy also outlined its plans for a successful holiday season, including empowering its floor staff with the ability to match online prices and giving extra compensation to the best performing workers.
But ITG analyst John Tomlinson said results for the fourth quarter will be key to see if Joly's plans for the company will pay off.
"He's saying the right things about what Best Buy's problems are, but the devil is in the details," Tomlinson said. "Until you actually see the sales lift and benefit from those investments, most investors are going to take a wait-and-see-type approach."