On the data front, the August trade deficit came in at $48.3 billion, the widest in five months.
The International Monetary Fund trimmed its global growth forecast for 2015 from 3.3 percent to 3.1 percent, citing weaker growth prospects for emerging economies.
Treasury yields spiked before holding lower, with the 10-year at 2.04 percent and the 2-year at 0.60 percent.
The Treasury Department auctioned $24 billion of 3-year notes at a high yield of 0.895 percent.
The dollar fell more than half a percent against major world currencies, with the euro at $1.12 and the yen at 120.2 yen against the greenback.
U.S. stocks closed more than 1.5 percent higher Monday, extending Friday's surprise intraday reversal, as investors digested the implications of the jobs data on the timing of a rate hike and awaited quarterly earnings.
While some analysts said the gains were a technical bounce from correction levels, others said the recovery was helped by expectations of easy monetary policy from the weaker-than-expected jobs report. After the monthly nonfarm payrolls report, Fed funds futures were pricing in expectations that the first rate hike will come no earlier than March 2016.
All three major averages held within 10 percent of their 52-week highs, or out of correction territory. The Russell 2000 remained in correction mode.
"There's a good possibility as the first few earnings begin to creep in we could approach 2,000 (on the S&P 500) and cross above that," Cardillo said.
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In Europe, stocks ended higher Tuesday following gains in oil, mostly shaking off poor industrial data out of Germany.
In Asia, the Nikkei closed 1 percent higher as investors digested news of agreement on the historic Trans-Pacific Partnership and awaited the outcome of the Bank of Japan's policy meeting Wednesday. The Trans-Pacific Partnership trade deal among the United States, Japan and 10 other Pacific Rim countries still needs approval from the U.S. Congress.
The Dow Jones Industrial Average closed up 13.69 points, or 0.08 percent, at 16,790.12, with UnitedHealth leading decliners and DuPont leading advancers.
The S&P 500 closed down 7.13 points, or 0.36 percent, at 1,979.92, with health care leading seven sectors lower and energy the greatest advancer.
The Nasdaq closed down 32.90 points, or 0.69 percent, at 4,748.36.
The CBOE Volatility Index (VIX), widely considered the best gauge of fear in the market, held just below 20.
About eight stocks advanced for every seven decliners on the New York Stock Exchange, with an exchange volume of 997 million and a composite volume of 4.1 billion in the close.
Gold futures settled up $8.80 at $1,146.40 an ounce.
—CNBC's Peter Schacknow contributed to this report.