In corporate news:
Alibaba — Barron's cover story said the stock could plunge 50 percent from current levels based on its price-to-earnings ratio with other tech companies, market share, and other factors. The Chinese e-commerce giant responded with a letteron its website outlining what it considered inconsistencies in the article's analysis. The stock closed down 3.1 percent.
Read MoreAlibaba warned there was trouble before Barron's
Apple — Pre-order demand for the iPhone 6s and 6s Plus on their first day of availability was stronger in China than most regions, according to early reports. The company said in a statement it is "on pace to beat last year's 10 million unit first-weekend record when the new iPhones go on sale Sept. 25."
Read More Early movers: BABA, SLH, AAPL, MRVL, FCAU, HRB, FB, GOOG & more
The Dow Jones Industrial Average closed down 62.13 points, or 0.38 percent, at 16,370.96, with Cisco leading decliners and Apple leading a handful of advancers.
The S&P 500 closed down 8.02 points, or 0.41 percent, at 1,953.03, with materials leading nine sectors lower and utilities the only advancer.
The Nasdaq closed down 16.58 points, or 0.34 percent, at 4,805.76. The iShares Nasdaq Biotechnology ETF (IBB) briefly fell more than 1 percent.
The CBOE Volatility Index (VIX), widely considered the best gauge of fear in the market, traded near 24.
About two stocks declined for every advancer on the New York Stock Exchange, with an exchange volume of 683 million and a composite volume of 2.9 billion in the close.
Gold futures settled up $4.40 at $1,107.70 an ounce.
—CNBC's Robert Hum contributed to this report.