Weak investor appetite amid volatile markets contributed to Suntory Holdings pricing its food and soft drinks unit at 3,100 yen ($31.68) per share, at the bottom end of a 3,000-3,800 yen per share range.
Still, the IPO is Asia's biggest so far this year, followed by a $2.1 billion IPO by the infrastructure fund of Thai firm BTS Group Holdings in April. It is also the second largest IPO globally after a $5 billion listing of Brazilian financial services firm Seguridade Participacoes earlier this year.
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Suntory Beverage and Food, well-known in Japan for drinks such as its BOSS canned coffee, will make its market debut in Tokyo on Wednesday. The parent company's beer unit is not included in the IPO.
"We are in a period of correction, so it's not a great time to list but I do think appetite towards Japanese shares will pick up," said one Japan-based trader.
Japanese stocks, propelled higher since last November by expectations foraggressive monetary stimulus from the country's central bank and optimism about growth prospects, have fallen back in the past month.
The benchmark Nikkei is down about 13 percent from a 5-1/2 year high set in May as concerns about an unwinding of U.S. monetary stimulus and China's economic growth dent major stock markets across the world.
Profit taking on the Nikkei's double-digit gains this year and caution regarding the success of the country's economic policies have also contributed to volatility in Japanese shares.
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Analysts however were more hopeful about the outlook.
"The thing about this IPO is that it's new paper being issued in an unfortunate market. It's just bad timing," said Ben Collett, the head of Asian equities at Sunrise Brokers in Hong Kong.
"We do think Suntory is a decent buy and it is a good time to get back into Japanese stocks versus other Asian markets, versus the U.S., versus Europe," he added.
Even with its recent retreat, the Nikkei is up 33 percent so far this year, compared with a 14 percent rise in the S&P 500 index of U.S. shares.
- By CNBC's Dhara Ranasinghe; Follow her on Twitter: