The index also showed that prices fell 1.7 percent from the previous three-month period, the largest quarter-to-quarter decline in the index's history.

The S&P/Case-Schiller quarterly index tracks prices of existing single-family homes across the nation compared with a year earlier.

A separate index that covers 20 U.S. metropolitan areas dropped 4.9 percent in September from a year earlier, with 15 metro areas posting declines. Only five metro areas—Atlanta, Charlotte, N.C., Dallas, Portland, Ore., and Seattle—showed an increase in prices, but S&P noted that the pace of the rise is decelerating.

Tampa and Miami led the index with the lowest year-over-year declines at 11.1 percent and 10 percent, respectively. It also showed drops in San Diego of 9.6 percent; Detroit, 9.6 percent; Las Vegas, 9 percent; Phoenix, 8.8 percent; and Los Angeles, 7 percent.

The S&P's 10-area index decreased 5.5 percent in September from the previous year.

Last week, the National Association of Realtors said that sales of existing homes fell in 46 states in the third quarter. However, the trade group said home prices rose in 93 of the 150 metropolitan areas surveyed.

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