Hisao Tanaka and vice chairman Norio Sasaki -- also a former president -- stepped down after an independent report found senior management complicit in a years-long scheme to pad profits.
In a stinging indictment, the report by a company-hired panel said managers were involved in "systematically" inflating profits over several years, in one of the most damaging accounting scandals to hit Japan in recent years.
"Because of this Hisao Tanaka, our company president, and Norio Sasaki, our company's vice chairman... Will resign today."
Tanaka, 64, and Sasaki, 66, both joined Toshiba in the early Seventies.
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Sasaki served as Toshiba president between June 2009 and June 2013, covering most of the period during which the company inflated the profits.
Chairman Masashi Muromachi will take over as president in the interim, the company said.
They will also deal another blow to corporate Japan's image after a huge scandal at camera and medical equipment maker Olympus. In 2013, a trio of former executives at the firm were handed suspended jail for their roles in a USD 1.7 billion accounting fraud.
That story grabbed international headlines as its first foreign executive exposed the cover up that led to his colleagues' downfall.
The Toshiba panel, headed by a former Tokyo prosecutor, painted the picture of a corporate culture where underlings could not challenge powerful bosses who were intent on boosting profits at almost any cost.
"Toshiba had a corporate culture in which management decisions could not be challenged," it added.
Despite the storm engulfing the company, Toshiba shares jumped today as the report ended months of uncertainty about the extent of the accounting problems, and who was to blame.
The Tokyo-listed shares soared 6.13 per cent to 399.90 yen by the close.
Analysts said the share price jump was the result of investors buying back into the battered stock, which had lost more than 20 per cent since May.