Nintendo rose by 1.6% following the 17.7% plunge on Monday.
While the Pokemon franchise is owned by Nintendo, the developer of the game is US company Niantic.
Nintendo's market value more than doubled at one point due to the huge success of Pokemon Go.
Despite seeing its sharpest drop in more than 25 years on Monday, the firm's shares are still up more than 60% from before the 6 July launch of Pokemon Go.
On the wider market, Japan's Nikkei 225 index fell 1.4% to close at 16,383.04.
The losses come ahead of a Bank of Japan meeting at the end of the week, which is expected to give clues about a new stimulus package promised by Prime Minister Shinzo Abe.
Hong Kong's Hang Seng index rose 0.6% to close at 22,129.73 led by financial and consumer stocks.
Over on the mainland, the Shanghai Composite gained 1.14% to end at 3,050.17.
Shares in South Korea gained ground, with the country's benchmark Kospi index ending 0.8% higher at 2,027.34.
Investor sentiment was lifted by fresh growth data showing that South Korea's economy grew at 3.2% in the second quarter, beating expectations.
Shares in SK Hynix, though, lost 1.4% after the world's second-biggest chipmaker said its second-quarter operating profit fell 67% from a year earlier due to weaker demand.
In Australia, the ASX 200 share index closed flat at 5,537.50.
Shares in Japanese games company Nintendo increased slightly after record losses on Monday when it had warned that the Pokemon Go success would have a limited impact on profits.