Energy fell almost 2.5 percent to lead nearly all S&P 500 sectors lower. Only utilities held slight gains.
U.S. crude settled down 57 cents, or 1.6 percent, at $34.95 a barrel, its lowest since February 2009. Brent settled about 0.9 percent lower at $37.06 a barrel, its lowest in nearly seven years.
Natural gas ended 1.96 percent lower at $1.755, its lowest since March 1999.
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"The markets are a little worried about how strong the U.S. economy is, how much strong dollar it can take, and commodities (declining) again," said John Bredemus, vice president at Allianz Investment Management.
The U.S. dollar held about 1.3 percent higher against major world currencies, with the euro near $1.081. The yen was near 122.71 yen against the greenback in the close.
Gold futures for February delivery settled down $27.20 at $1,049.60 an ounce. Newmont Mining and Freeport-McMoRan plunged 7.7 percent and 8.5 percent, respectively, to lead decliners in materials, the second-greatest laggard in the S&P. Copper also declined.
Treasury yields held a touch lower, with the 2-year yield below 1 percent and the 10-year yield around 2.23 percent.
As most expected, the U.S. central bank on Wednesday raised its target funds rate by a quarter point, while emphasizing a gradual and data-dependent pace of future tightening. The hike was the first since June 2006.
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"It was pretty much everything they said they were going to do. Obviously the rate hike was a quarter-point which they telegraphed, and (they remained) accommodative," said Peter Coleman, head trader at Convergex.
"The continued problem we have is still oil going down. ... If you see a significant drop in oil you probably see a drop in the market again on a short-term basis," he said. Still, "you got some certainty (on the Fed). You may see some sector rotation."
U.S. stocks rallied after the Fed announcement Wednesday afternoon to close sharply higher, with the S&P 500 in the green for 2015. Stock index futures traded higher ahead of the open, following overnight gains in overseas equities.
European stocks ended higher, off session highs, while Asian equities closed higher with the Nikkei up more than 1.5 percent.
Nick Raich, CEO of The Earnings Scout, said the Fed's move is "not going to remove macroeconomic uncertainty."
"Most of the economic data, revenue data we've collected is not getting better. It's getting worse. The uncertainty is not being lifted by any measure for the overall economy," he said.
In economic news, the Philly Fed index for December was minus 5.9, the lowest of the year after a positive 1.9 print in November.
Leading indicators for November showed a 0.4 percent rise, with October unrevised, up 0.6 percent, according to StreetAccount. Initial claims came in at 271,000.
The U.S. current account deficit in the third quarter increased 11.7 percent to $124.1 billion, its highest level in nearly seven years, as a strong dollar weighed on exports and the profits of multinational corporations, the Commerce Department said.