"It's been very smooth," Duncan Niederauer, CEO of NYSE Euronext, told CNBC from the exchange floor shortly after the opening bell. "The market-making community is more than staffed enough to be open."
The last time the New York Stock Exchange closed for two consecutive days because of weather was during the Blizzard of 1888 124 years ago. Since power was out in large parts of downtown Manhattan on Wednesday, the trading floor had to be run on backup generators.
Home Depot and Lowe's rose as investors anticipated more business for the home improvement chains as people made repairs in the aftermath of the devastating storm. Home Depot gained $1.34 to $61.38 and Lowe's rose $1.02 to $32.38.
Netflix soared $9.66 to $79.24 after financier Carl Icahn said he had bought a 10 percent stake in the troubled company.
Among the losers were insurers Chubb, Allstate and Travelers. Investors worried that the companies are most likely to suffer losses due to insurance claims. The trio have a large share of the insurance market in areas where Hurricane Sandy hit.
Chubb fell 98 cents to $76.98, Travelers dropped 62 cents to $70.94 and Allstate slipped 17 cents to $39.98.
Half of the ten industry sectors in the S&P 500 fell. Health-care stocks were down 0.7 percent, the biggest drop. Utility stocks led the gainers with a rise of 0.8 percent.
Stocks flitted between small gains and losses in the last hour of trading. The indexes started the day higher than the close on Friday, the last trading day. Then they dropped, and stayed in the red for much of the day.
The tech-heavy Nasdaq composite lost 10.72 points to 2,977.23.
The opening followed days of scrambling by NYSE officials to make sure power, telecom connections and computers would be ready. Many workers on the floor use the subways to get downtown, but Hurricane Sandy left the system with its worst damage in its 108-year history. New York's governor, Andrew Cuomo, said says limited subway service will resume in New York City on Thursday.
About three stocks rose for every one that fell on the New York Stock Exchange. Trading volume was 3.4 billion shares, in line with the recent average.
The yield on the 10-year Treasury note fell to 1.69 percent from 1.72 percent at midday Monday. Bond trading was closed Tuesday and ended early Monday because of the storm.
Among other stocks making big moves:
Facebook fell 83 cents to $21.11, a loss of nearly 4 percent. Facebook employees became eligible this week to sell restricted stock for the first time. Up to 1.5 billion more shares could be sold, about 3.5 times the 421 million shares that had been trading since Facebook's initial public offering in May.
General Motors jumped $2.22 to $25.50 after the company reported a turnaround in its South American business and gave a brighter outlook for sales in Europe. GM posted better-than-expected results internationally outside of China
Apple fell $8.68 to $595.32. The Wall Street Journal reported that the head of Apple's iPhone software development was asked to resign after he refused to sign a letter apologizing for the flaws of Apple's mapping application.