The benchmark Nikkei 225 index inched down 0.06 percent or 18.16 points to end at 29,048.02, while the broader Topix index advanced 0.15 percent or 3.02 points to 1,965.67.
The reassignment of director candidates for the audit, nominating and compensation committees follows an explosive shareholder-commissioned investigation that accused Toshiba and the government of colluding to pressure foreign investors.
Satoshi Tsunakawa, who led the company before Kurumatani and until Wednesday was chairman, will once again assume the helm.
The offer sparked a strong backlash from Toshiba managers, prompting them to lobby against it to the government, said one of the sources. The sources declined to be identified due to the sensitivity of the matter.
In a statement welcoming the result, Effissimo said independent investigators will have "a broad mandate" to examine last year's AGM, and Toshiba's directors and executives have a legal obligation to cooperate.
Toshiba has been dogged by years of scandals including accounting misdeeds and a huge writedown for its US nuclear business that it eventually withdrew from.
Toshiba said last month it had made no change in its policy on investment and shareholder returns. It says the issue is the result of a "misunderstanding" by the shareholder.
In its presentation regarding its call for an extraordinary meeting, Farallon said: "This shift in policy, and the apparent backpedaling, has led to further trust issues and concerns."