The benchmark Nikkei share average <.N225> rose 0.11% to 23,626.73, while the broader Topix lost 0.32% to 1,643.90.
Tokyo shares followed Wall Street lower in early trade before reversing course in the afternoon, which analysts suspected was due to the Bank of Japan's exchange-traded fund buying.
On Tuesday, major indexes on Wall Street ended lower as Johnson & Johnson and Eli Lilly and Co halted coronavirus vaccine and antibody treatment trials, respectively, over safety concerns, dampening investor sentiment.
Fading hopes for a new U.S. coronavirus relief package also weighed on the market, as U.S. House Speaker Nancy Pelosi rejected a $1.8 trillion coronavirus relief proposal from the White House.
Back home, Apple-related issues underperformed on profit-taking and dented by a 2.7% fall in Apple Inc shares following an event where the company unveiled its latest iPhone.
TDK Corp edged 0.08% lower, while Taiyo Yuden fell 0.27%.
Financial shares also took a hit from a weak performance in their U.S. peers, with Sumitomo Mitsui Financial Group dropping 1.71% and Mitsubishi UFJ Financial Group down 1.01%.
Meanwhile, semiconductors performed strongly, with Tokyo Electron Ltd rising about 2.6% and Lasertec Corp up 0.1%.
"The moves are quite subtle when only looking at the Nikkei share average. But the Mothers Index is renewing highs and semiconductor stocks are still strongly sought after," said Takashi Hiroki, chief strategist at Monex Securities.
The Mothers Index of start-up firms gained 1.37%, posting its highest close since January 2018.
Elsewhere, ANA Holdings dipped 4.59% after reports that the company was going to cut monthly wages for all workers by 5%.
Nippon Steel lost 3.82% on news that the company would sell two U.S. plants as it speeds up a reorganisation in overseas operations.
(This story corrects Eli Lilly trial in paragraph 4 to antibody treatment, not vaccine)
(Reporting by Eimi Yamamitsu; Editing by Subhranshu Sahu)