Ghosn's defence team had made the bid for his release on the basis that one of the charges against him, an alleged breach of trust of the company, was null and void.
But his hopes of being granted bail appear dim, with his chief lawyer admitting at a recent news conference that his client could stay in detention for at least another six months until his trial begins, citing the complexity of a case involving documents in both Japanese and English.
Ghosn has strongly denied the allegations against him.
Kelly and Nissan were not charged with breach of trust.
Ghosn, 64, says he's innocent.
But even Ghosn's lead lawyer Motonari Otsuru had earlier said it would be "very difficult" to secure bail.
Ghosn's aide Greg Kelly, who was arrested at the same time over his alleged role in helping the executive understate his pay, was released on a bail at $635 000 (over R8m) on December 25. His current detention term is scheduled to end on Friday.
The court overturned a ban on family visiting rights, meaning Ghosn can receive visits from his loved ones, as well as his legal team and diplomats.
He said the compensation was never decided on, the investment deal did not result in any losses to Nissan, and the payments to the Saudi businessman was for legitimate services related to dealers and investments in the Gulf.
Nissan CEO Hiroto Saikawa told reporters later in the day that an ongoing internal probe into the alleged misconduct by Ghosn, who holds Brazilian, French and Lebanese nationality, will be conducted together with Renault. It declared that no fraud was found in 2017-2018 but it is still examining previous years.
Renault, which is the biggest shareholder in Nissan, has refrained from removing Ghosn, instead appointing interim replacements.
"I am pleading with the Japanese authorities to provide us with any information at all about my husband's health. We are fearful and very anxious his recovery will be complicated while he continues to endure such harsh conditions and unfair treatment", she said.
At the end of the almost two-hour hearing, his lawyers applied for him to be freed but the court slapped this down, arguing he was a flight risk and could tamper with evidence if released. Such visits were canceled Thursday but resumed Friday.
Both the Tokyo Prosecutors Office and Nissan declined to comment on the issues when contacted by Reuters.
Ghosn holds French, Lebanese and Brazilian passports and his children live in the United States, his wife said that her husband is living in "harsh conditions" and enduring "unfair treatment", and that authorities have not let the family speak with medical personnel at the detention center.