"What bothers the markets are uncertainties about a new president, his issues of trade, and people are worried about how other world actors will react to a Trump presidency," if he wins, said Strategas head of policy research Dan Clifton.
NBC News projected Republicans will retain control of the House and the Senate. Wall Street has favored a win by Clinton but Republican control of Congress.
In Asia, the Nikkei was down more than 4 percent, erasing a more than 1 percent gain on the day.
The Mexican peso, which has been a proxy for Trump, was down sharply against the dollar, after rallying during the U.S. trading day. Trump has said he would build a wall along Mexico's northern border and break trade deals with the country. The U.S. dollar also gave up early gains against the yen and Swiss franc.
While voting finished in the Western states, the markets reacted as if Trump was heading to victory after trading higher for two days on optimism that Clinton could win.
"I think this could be the second strike of populism if Trump wins and I think that it's probably a bigger surprise for international markets than it for the U.S.," said Jack Ablin, CIO at BMO Private Bank. "Right now it's just emotional. Everything from the last two days would get undone, and then we'd have to take it down. We could see a 600 point (Dow) reversal."
Wall Street has favored a Clinton win because of some of Trump's policies, such as his positions on trade.
"Emerging markets will just get annihilated. Oil gets hammered, and we'll see. ... It's still early," said Ablin.
Gold futures also traded higher in a safety play, rising 2.19 percent, or $27.90, to $1,302.40 per ounce.
—CNBC's Kate Kelly contributed to this report.