The Nikkei share average ended 0.4 percent higher at 15,919.58 after trading in negative territory in the morning.
China's stock market rose the most in two weeks on Wednesday, reversing from early losses as investors shrugged off MSCI's decision not to add mainland shares to one of its key benchmark indexes.
Traders said investors had already been bracing for a "no" decision, as reflected by Monday's market tumble of more than 3 percent, with some bargain hunting in the process.
The blue-chip CSI300 index rose 1.3 percent, to 3,116.37, while the Shanghai Composite Index gained 1.6 percent, to 2,887.21 point
MSCI said it decided not to add local Chinese shares to its key emerging market index as Beijing had more work to do in liberalising capital markets.
Hong Kong shares rose on Wednesday, drawing optimism from a rebound in mainland markets
But the Hong Kong market remains under pressure, with investors worried about global growth, and the prospect of Britain voting next week to leave the European Union.
The Hang Seng index rose 0.4 percent, to 20,467.52, while the China Enterprises Index gained 0.3 percent, to 8,609.59 points.
Reuters
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