The benchmark Nikkei 225 index rose 0.37 percent, or 80.40 points, to 22,091.18, while the broader Topix index edged up 0.08 percent, or 1.35 points, to 1,652.07.
The market swung in and out of positive territory in the morning as investors fret about geopolitical tensions such as a brewing US-Russia nuclear row and China's struggling economy.
But bargain-buying and a rally in Shanghai provided support in the afternoon, lifting the Nikkei index into the green by the closing bell, Okasan Online Securities said in a note to clients.
"Investors cheered the rise of Chinese shares and brought (the Nikkei) back to positive territory. The index hovered in a narrow range just above 22,100 towards the end of the day," it said.
The dollar was at 112.51 yen from 112.41 yen in New York late Tuesday, helping exporters.
SoftBank ended 0.52 percent higher at 9,205 yen following reports that its founder Masayoshi Son had skipped an investment forum in Saudi Arabia but had met crown prince Mohammed bin Salman.
Top automaker Toyota also added 0.52 percent to 6,578 yen and Uniqlo-operator Fast Retailing rose 2.20 percent to 57,230 yen but Nintendo fell 1.01 percent to 37,140 yen.
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