Under the deal, SoftBank will buy 221 billion yen ($2 billion) of Yahoo Japan shares from Altaba, formerly Yahoo Inc. Yahoo Japan will then buy back 220 billion of stock from SoftBank.
As a result of the transaction SoftBank's stake in Yahoo Japan will rise to 48.17 percent from 42.95 percent with just a $9 million net investment. Altaba, Yahoo Japan's second largest shareholder, will have about 27 percent and end a joint venture partnership.
SoftBank and its Vision Fund, the world's largest private equity fund standing at over $93 billion as of May last year, have been taking minority stakes in technology companies around the world that Son believes will come to dominate their respective fields.
The news of the Yahoo Japan deal comes as SoftBank prepares to list its domestic telecoms unit in what could be the largest Japanese IPO in nearly two decades.