The company's 16.1 billion yen ($157 million) deal to sell the real estate to Sumitomo Realty and Development will be completed next month, it said.
The properties are in the Gotenyama area near the city's Shinagawa railway station, where land prices have been on the rise recently.
In 2007, the firm sold a portion of the site, moving its headquarters to the opposite side of Shinagawa station.
Sony started as Tokyo Tsushin Kogyo in 1946, the year after Japan's defeat in World War II. The following year it moved from a different site in the capital to the Gotenyama area, where it grew into a global player built on its groundbreaking Walkman and popular televisions.
A museum archiving Sony's epoch-making products will be one of its few remaining properties there.
The deal Friday comes after Sony said last year it was selling its US headquarters in Manhattan for $1.1 billion as it looks to recoup from four consecutive years of losses.
Sony and domestic rivals Panasonic and Sharp have faced severe competition from abroad in their hard-hit consumer electronics units and have been undergoing painful restructurings to move past years of losses.
Despite returning to profit in its latest fiscal year, Sony is braced for a $1.08 billion loss in the 12 months to March as it plans to cut 5,000 jobs and exit the stagnant PC market.
On Friday, Sony said the real-estate sale would not affect its earnings forecast for the current fiscal year.
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