The Japanese conglomerate said it had sold its 4.6% stake in the elevator maker for €864.7m ($946.2m; £607.6m).
The deal comes a day after Toshiba's president resigned amid an accounting scandal regarding overstated profits.
In a statement, the firm said the sale would help "efficient use of the company group assets" and "improve its balance sheets".
Kone on Wednesday announced the resignation of board member Kazunori Matsubara, formerly president of Toshiba Elevators, who had joined the board in February 2015.
The Finnish company said the sale of the shares and the resignation had "no other effect on the strategic alliance" between the two companies.
On Tuesday, Toshiba chief executive and president Hisao Tanaka and vice-chairman Norio Sasaki both stepped down after an independent panel found the firm had overstated its operating profit by a total of 151.8bn yen ($1.22bn, £780m) over a six-year period from 2008.
The overstatement was roughly triple an initial estimate by Toshiba.
The computers-to-nuclear conglomerate's shares dropped by 1.7% on Wednesday after their rally of 6% on Tuesday, the day the resignations were announced.
Toshiba has sold its stake in Finnish firm Kone in a bid to bolster its books amid the recent accounting scandal.