The index lost 2.27% to reach 19,416.06 points, its lowest level since December 2018.
The broader Topix index lost 1.53% to reach 1,385.12 points, its lowest point since November 2016.
Earlier, the Dow Jones Industrial Average, the broadest equities gauge on the New York Stock Exchange, closed up 1,167 points, or 4.9 percent, at 25,018. The Dow fell 2,014 points on Monday, its most ever in a day, closing 7.8 percent down after a crash in oil prices and panic selling induced by fears over the coronavirus.
On Monday, coronavirus and OPEC+ failure to agree on a deal extension sent global markets into a tailspin. However, on Tuesday, major European stock indexes closed down 0.3-1.5 percent after dropping around 8 percent the previous day.