The Bank of Japan, under pressure to calm the markets, said it has supplied an additional 41 billion yen Monday to financial institutions operating in areas hit by the earthquake and Tsunami. Nonetheless, trading in theyen remained choppyand was expected to stay that way.
Japan's strongest earthquake on record shutrefineries and industrial plants in the world's third-largest oil consumer. U.S. refiners, meanwhile, gained, including Tesoro , Western Refining and Frontier Oil . (Click here for more news on the disaster in Japan).
Solar stocks also gained, due to renewed concerns over the use of nuclear power, which had been regaining popularity as a no-carbon fuel alternative. LDK Solar , FirstSolar and JA Solar all advanced.
GE , which has nuclear ventures with Hitachi, declined more than 2 percent, although Citigroup wrote in a note that the decline was "excessive," given GE's limited exposure to financial losses due to the devastating problems with Japan's nuclear reactors, and given the fact the nuclear power business represents just 3 percent of GE sales. S&P Equity, meanwhile, reiterated its "buy" rating on the stock.
"We believe the share price reaction reflects headline risks rather than an accurate assessment of GE's financial exposure," Citi wrote, adding that investors could also be taking profits as GE shares had risen 11 percent before today's move.
Expectations that proposed or planned nuclear power plans may not go forward hurt utilities, however. Entergy , which currently generates nuclear power, sank more than 4 percent, after Bank of America Merrill Lynch downgraded the utility to "underperform" from "neutral," and cut its price target to $74 a share from $78, because of the uncertainty of nuclear power plant approvals that are "critical to long-term earnings."
The brokerage also downgraded Scana to "underperform" from "neutral," saying it has a "meaningful amount of its earnings growth tied to nuclear" through the utility's 55 percent share of two new units that were to contribute "almost all its earnings growth over the next five years."
The Southern Company may also experience delays in developing nuclear power as a result of the nuclear disaster in Japan, according to Citigroup.
Shares of Toyota , which said it would suspend production at all its car plants until at least March 16, dropped more than 4 percent. Rivals Honda and Nissan also fell. (Read more: Prius Production Delays Could Curb Toyota Rebound.)
Financials including Citigroup and JPMorgan slipped to lead markets lower in part over investor fears that Japan's quake will affect earnings of banks with global operations, said Dave Rovelli, Canaccord Genuity's managing director of equity trading.
The Stoxx 600 European Insurance Share Index fell about 1.5 percent. The reinsurers fared the worst, falling as much as 3.8 percent. Construction and refinery shares rose in emerging markets as investors expected a boost from large-scale reconstruction efforts.
U.S. insurers with exposure to Japan declined. Aflac and Hartford Financial both tumbled.
Boeing shares slipped after the company said if the firm's Japanese suppliers are disrupted by more than several weeks, the Dow component could face new production problemsfor the already long-delayed 787 Dreamliner.
Other Japanese stocks hit hard by the uncertainty caused by the quake were Panasonic , Sony and Toshiba .
And luxury goods makers heavily dependent on sales in Japan were also hit, including Coach and Tiffany , which both sank more than 5 percent.
Meanwhile, on the M&A front, Berkshire Hathaway agreed to buy Lubrizol for $135 a share, for about $9 billion in cash, the companies said. Lubrizol shares soared more than 25 percent. (Read more: Buffet Hits Mark With Latest Acquisition).
And Apple shares traded flat after analysts estimated the tech giant sold close to 1 million units of its new iPad 2 during its debut weekend.
Semiconductor stocks were mixed as investors struggled to understand how the quake would affect the sector, according to Scott Redler, chief strategic officer at T3Live.com. "This is a sector to watch going forward for the next few weeks," Redler said in a note to clients.
Micron Technology, Nvidia and National Semiconductor gained, while AMD and Xilink fell.
Pfizer advanced after reports the drug company may shed assets, according to Sanford C. Bernstein.
Family Dollar rose after news Nelson Peltz of Trian Fund Management reiterated its offer for the company, and said in an SEC filing that it was upset with the board of the discount retailer for adopting a "poison pill" defense against a takeover.
Volume on the consolidated tape of the New York Stock Exchange was 4.1 billion shares, while 964 million changed hands on the NYSE floor.
Gold rose slightly on Monday to close at $1,424.60 an ounce. The dollar , meanwhile, fell against a basket of currencies, as the euro gained on news inflation is rising in the region.
There is no major economic news on the calendar today, but the Federal Reserve's policy setting committee was expected to hold a one-day meeting on Tuesday. While the Fed is not expected to raise rates, the meeting will refocus traders on the central bank's bond buying program, set to end in June.
Producer prices and consumer inflation data are expected Wednesday and Thursday.
European shares fell to the lowest close since December in the wake of the Japan quote as investors feared the effects on growth and demand.
On Tap Next Week:
TUESDAY: Credit card default rates, Empire state manufacturing survey, import & export prices, housing market index, and FOMC meeting announcement.
WEDNESDAY: Mortgage applications, housing starts, producer price index, current account, and oil inventories.
THURSDAY: Consumer price index, jobless claims, industrial production, leading indicators, Philadelphia Fed survey, natural gas inventories, money supply; before-the-bell earnings from FedEx and Lululemon; after-the-bell earnings from Nike.
FRIDAY: Quadruple witching; before-the-bell earnings from Allianz.
More on CNBC.com