Major indexes also posted losses for the month, but ended the quarter with gains.
The S&P energy index was down 1.2 per cent on Tuesday following a more than 3 per cent drop in US oil prices. The S&P materials index also fell 1.2 per cent. Shares of Chevron, down 1 per cent at $119.32, were the biggest drag on the S&P 500.
The Thomson Reuters Jefferies CRB commodity index ended down 1.6 per cent, its largest daily decline since June 2013.
EBay, up 7.5 per cent at $56.63, was the S&P 500's biggest percentage gainer for the day, helping to limit losses. The company announced a plan to spin off its PayPal unit.
US consumer confidence fell in September for the first time in five months and home prices in July rose less than expected from a year earlier, underscoring the unsteady nature of US growth.
Analysts are skeptical of how many more gains are in store for the market this year, with the S&P 500 up 6.7 per cent since December 31 and third-quarter earnings still ahead.
"The market continues to be very resilient, but it's a monster market. I think you could have a weaker fourth quarter than you've gotten used to, and I think we've made our highs for the year already," said Uri Landesman, president at Platinum Partners in New York.
Apple shares rose 0.6 per cent to $100.75 after China approved iPhone 6 sales to begin October 17.
The Dow Jones industrial average fell 28.32 points, or 0.17 per cent, to 17,042.9.
The S&P 500 lost 5.51 points, or 0.28 per cent, to 1,972.29.
The Nasdaq Composite dropped 12.46 points, or 0.28 per cent, to 4,493.39.
For the month, the Dow was down 0.3 per cent, the S&P 500 was down 1.5 per cent and the Nasdaq was down 1.9 per cent. For the quarter, the Dow rose 1.3 per cent, the S&P 500 gained 0.6 percent, and the Nasdaq climbed 1.9 per cent.
Among the most active stocks on the NYSE were Ford Motor, down 2.12 per cent to $14.79, a day after its disappointing profit forecast.
Besides eBay and Apple, the most actively traded stocks on Nasdaq included Move Inc, up 37.1 per cent at $20.96.
Declining issues outnumbered advancers on the NYSE by 1,942 to 1,133, for a 1.71-to-1 ratio on the downside; on the Nasdaq, 1,864 issues fell and 824 advanced for a 2.26-to-1 ratio favoring decliners.
The benchmark S&P 500 index posted 15 new 52-week highs and 18 new lows; the Nasdaq Composite recorded 42 new highs and 138 new lows.
About 7.2 billion shares changed hands on US exchanges, above the 6.1 billion average for the last five sessions, according to data from BATS Global Markets.
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