It is yet another blow for the firm that has seen sales plunge and been forced to slash jobs since Ghosn's stunning arrest for allegedly hiding part of his salary from official documents to shareholders.
Hiroto Saikawa said he would leave the company on September 16, following the results of an investigation into excess pay he received after altering the terms of a bonus.
Saikawa is suspected of improperly adding 47 million yen ($440,000) to his compensation under a scheme in which directors can earn a bonus if their company's share price rises above a certain level in a set period.
Nissan officials were keen to stress that there was no illegality but that he should not have delegated the task to a junior executive.
"At the end of the day, the operation which should have been carried out by the president himself was... delegated to others, which is a violation of the rules," said Motoo Nagai, a board member.
Saikawa admitted handing the task to a company secretariat and said he was "not proud" of this but insisted it was not the same as the misconduct of which Ghosn is accused.
He was it was "totally different from the intentional wrongdoing that was uncovered" during the internal Nissan probe into Ghosn and his right-hand man, US executive Greg Kelly. The controversial "share appreciation" scheme has now been scrapped, the Nissan board announced.
Current chief operating officer, Yasuhiro Yamauchi, will take over as acting CEO on September 16, when Saikawa officially leaves, and Nissan hopes to find a permanent replacement by the end of October.
The carmaker is currently undergoing an overhaul intended to strengthen governance after the Ghosn scandal.
In June, Nissan shareholders voted in favour of various measures including the establishment of three new oversight committees responsible for the appointment of senior officials, pay issues and auditing.
They also approved the election of 11 directors as the firm restructures, among them two Renault executives as well as Saikawa.
The reforms were designed to put Nissan on a more stable footing after the arrest of Ghosn, who has been sacked from his leadership roles at the Japanese firm and others.
He is awaiting trial on charges of under-reporting millions of dollars in salary and of using company funds for personal expenses.