The bench of Justice Anish Dayal has rejected the quashing petition filed by Ms Fernandez.
The court had reserved the decision in April after hearing arguments from all the parties in the case.
The Bollywood actor's counsel had claimed in the High Court that she was unaware of the illicit origin of gifts she received, which are allegedly part of a Rs 200 crore money laundering case involving the conman.
Her lawyer claimed that she did not know that the gifts were part of the proceeds of crime.
The Bollywood actress had also sought quashing of the second supplementary chargesheet of the Enforcement Directorate (ED) in the case and proceedings pending in a trial court.
However, the ED argued that her petition was not maintainable as a special court had taken cognisance of the chargesheet and prima facie found a case. While the same cognisance order of the trial court was not challenged by her.
Sukesh Chandrasekhar is currently lodged in jail for allegedly duping the spouses of former promoters of Ranbaxy, Shivinder Singh and Malvinder Singh of Rs 200 crore.
He is facing multiple investigations across the country over such cases.
According to the ED, Chandrasekhar and his wife Leena Paulose, allegedly used hawala routes and created shell companies along with other accused persons to park the money earned as proceeds of crime.
"It is also not the case of ED that she was aware that gifts she received were part of proceeds of crime," the actress's counsel had argued in court.
The ED has alleged that Ms Fernandez did not verify the newspaper article about Sukesh Chandrasekar. She received gifts from him.
However, Ms Fernandez's lawyer submitted that the actress came across the newspaper article in February 2019. But newspaper article is not evidence.
It was further claimed by her lawyer that she was convinced by co-accused Pinky Irani that Sukesh was being made a scapegoat as he had high political connections.