Automakers were in focus following June's strong U.S. auto sales data; Nissan Motor and Mazda Motor climbed over 1 percent each.
The country's biggest online retailer Rakuten rallied over 2 percent after AirAsia said on Tuesday that it would set up a low-cost airline with the Japanese firm.
Read MoreAirAsia Japan to turn a profit within a year: CEO
China shares up
Mainland shares gained 0.4 percent to finish at a two-week high thanks to strong gains in new market listings; Yixintang Pharmaceutical, Forbon Technology and Shapuaisi Pharmaceutical all soared in their first day of trade.
China Eastern Airlines rose over 1 percent after announcing that it has officially transformed its Beijing-based subsidiary China United Airlines into a budget carrier.
Read MoreChina's infamous swag markets lose their shine
Hong Kong stocks resumed trade at a near seven-month high following Tuesday's public holiday. Property developers led the gains with Henderson Land and Cheung Kong both 3 percent higher.
ASX 1.5% higher
Australia's S&P ASX 200 index finished at a one-week high, recovering from the previous day's two-and-a-half month low despite weak trade data. The economy posted a deficit of A$1.91 billion in May, below forecasts for a A$120 million deficit, which saw the Australian dollar retreat from Tuesday's seven-month high against the greenback.
Read MoreAussie dollar on a roll, but can it last?