Rakuten said the all-cash deal would give it access to 2.5 million new customers in the United States, Canada, South Korea and China.
"The company will acquire Ebates for a total consideration of USD 1 billion in cash, and will hold 100 per cent of Ebates outstanding voting stock," Rakuten said in a statement.
"The combination of the two companies will give birth to an attractive and innovative membership-based marketplace for consumers featuring a points programme at the core."
The deal could help Rakuten compete abroad with industry giants Amazon and China's Alibaba, which is preparing an initial public offering that could raise as much as USD 24.3 billion in what be the biggest share sale in history.
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San Francisco-based Ebates runs websites that offer rebates and coupons for shopping from 1,700-plus partner retailers, including Amazon and eBay.
It hosted about USD 2.2 billion in transactions in its 2013 fiscal year.
Rakuten has a credit-card-linked reward points system in Japan to help retain its customer base.
Since launching its business in Taiwan in 2008, Rakuten has expanded to more than 10 foreign markets.
But its foreign e-commerce transactions are a small share of its overall business, which is focused on a domestic market that is unlikely to offer much more room for growth.
Last year, Rakuten bought US video-streaming provider Viki for about USD 200 million while in February it picked up messaging app provider Viber for around USD 900 million.
Rakuten's Tokyo-listed shares ended down 1.25 per cent at 1,254.0 yen (USD 12) before the deal was confirmed.
However, the stock has been under pressure as investors questioned the size and merits of the reported deal, said Monex Group market analyst Toshiyuki Kanayama.
"It's not totally clear that it will add significantly to Rakuten's business," he told Dow Jones Newswires.
"Additionally, it also leaves room for speculation that Rakuten may turn to a potentially dilutive share offer in order to raise funds for the purchase.