But pre-holiday selling on the market's busiest day ever weighed on some recent gainers, such as real estate developer Mitsui Fudosan Co Ltd and nonlife insurer Millea Holdings Inc.
Japanese financial markets are closed on Thursday for Culture Day, a national holiday. A little over 3.7 billion shares changed hands on the Tokyo bourse's main board a day after a computer systems failure closed down share trading for most of the session at Asia's largest bourse.
Last year's daily average was 1.45 billion shares.
Fujitsu Ltd fell again, after the Tokyo Stock Exchange said the failure of trading-system software developed by Fujitsu was behind the bourse's worst-ever suspension of trade on Tuesday.
Some auto makers also lost ground following US data showing a fall in car sales.
The capital-weighted TOPIX index was up 0.08 percent at 1,474.25, its highest close since October 10, 2000.
The Nikkei 225-stock average was up 0.19 percent at 13,894.78, its highest close since May 24, 2001.
Analysts said investors were rotating their buying targets mainly among stocks dependent on domestic demand.
"Stocks such as insurance and real estate firms were avoided today only because they are out of the rotation," said Kazuhiro Takahashi, general manager at Daiwa Securities SMBC's equity planning and administration department.
"Expectations are strong for a further rally, with a consensus that the Nikkei will test the 14,000 level by the year end," he said.
Mitsui Fudosan, Japan's largest property developer, was down 1.8 percent at 1,934 yen. The company's bigger-than-expected profit for the April-September half had boosted the shares to 1,984 yen on Tuesday, the highest level in more than a decade.
No 1 non-life insurer Millea was down 0.5 percent at 2.11 million yen. It hit a lifetime high of 2.18 million last week.
Nissan Motor Co Ltd, Japan's second-biggest auto maker, lost 1.7 percent to 1,192 yen after US industry data late on Tuesday showed the company's auto sales fell 13.3 percent in October from a year earlier.
No 6 Mazda Motor Corp, whose US sales fell 4.7 percent in October, lost 2.9 percent to 545 yen despite solid earnings announced in the morning.
Fujitsu inched down 0.1 percent to 751 yen after falling 1.6 percent in the previous session.
In contrast, Minebea Co Ltd, Japan's biggest miniature-ball-bearing maker, soared 9.8 percent to 505 yen after UBS and Goldman Sachs separately raised their ratings in the wake of the company's earnings.
Sanyo Electric Co Ltd shot up 12.5 percent to 270 yen after the struggling electronics maker said an executive from its main bank would join its management, easing investor concerns about bank support.
The country's top three lenders all hit new lifetime highs.
Industry leader Mitsubishi UFJ rose 4 percent to 1.58 million yen and second-ranked Mizuho Financial Group Inc was up 1.7 percent at 847,000.
Mizuho raised $4.6 billion in Japan's largest share issue this year. Wednesday is the payment day for the issue at 696,780 yen per share, but few buyers hurried to lock in profits.