The move -- which also includes a ban on dolphin meat sales -- comes as Japan said Thursday it was cancelling this year's hunt for the first time in more than a quarter of a century to abide by the decision of the United Nations' Hague-based International Court of Justice this week.
Australia, backed by New Zealand, hauled Japan before the international court in 2010 in a bid to stop the yearly campaign, which has attracted widespread condemnation outside Japan.
"We issued a notice to all stores on April 1, asking them to stop sales of whale meat products by the end of the month," a Rakuten spokeswoman said.
"We made the decision... following the ruling by the International Court of Justice and a subsequent comment by the Japanese government that it will obey the ruling," she added.
The notice was issued to about 42,000 online shops that operate on Rakuten's digital marketplace, she said, adding the company did not have a figure for how many sold whale meat.
A search of the site Friday turned up about 700 listings for whale meat products. There were no listings for dolphin meat.
Tokyo had been widely criticised for using a legal loophole in a 1986 whaling ban that allowed it to continue slaughtering the mammals, ostensibly so it could gather scientific data.
However, it has never made a secret of the fact that whale meat from these hunts often ended up on dining tables.
Rakuten's move to ban the sale of whale-meat products appeared to go above and beyond the ruling, which said that Japan's hunt in the Southern Ocean was a commercial activity disguised as science.
The judgement did not affect whales hunted as part of Japan's coastal whaling programme or in the north Pacific.
Public consumption of whale meat in Japan has steadily and significantly fallen in recent years and there is little support for whaling itself.
But aggressive anti-whaling campaigns hardened sentiment among the Japanese public, who came to see the issue as an attack on differing cultural values.
Rakuten's decision comes several weeks after the Environmental Investigation Agency (EIA) published a critical report that said the e-tailer was the world's largest online marketplace for whale meat and elephant ivory, and said the advertisements were akin to arming poachers.
Rakuten said Friday there was no change to its online ivory sales, which are restricted to domestic shoppers.