The bench of Justice FRM Nazmul Ahasan and Justice KM Kamrul Kader passed the order on Wednesday.
Two officials of the BRAC Bank were blamed for the incident.
Advocate Khurshid Alam Khan appeared for the ACC while Barrister Sheikh Mohammad Asaduzzaman and Barrister Zakir Hossain for BRAC Bank Ltd and Sonali Bank respectively.
Khan said the HC also disposed of the rule asking the bank to provide compensation to Jaha Alam.
The bank has to pay the amount within 30 days.
The court also asked the ACC to be vigilant so that such mistakes do not happen in future as people have a lot of expectations from this organization, said the ACC lawyer.
Earlier on Tuesday, the court fixed the date after hearing law-point arguments from both sides.
On February 12, the court kept the matter as a case awaiting verdict (CAV) completing hearing on the rule asking the government to explain why directives should not be given to provide compensation to Jaha Alam in the loan default case filed by ACC.
Hailing from Tangail, Jaha Alam languished in jail for years in 33 cases instead of real culprit Abu Salek involving embezzlement of Tk 18 crore from Sonali Bank.
The HC took cognizance of the matter following a newspaper report that an innocent suffers due to faults of another.
The High Court passed a suo moto order following the newspaper report.
Jaha Alam was released on bail granted by the apex court on February 3 this year.
Also read: Jaha Alam Ordeal: HC fixes Wednesday for delivering verdict