Rath broke down in the court as presiding officer I J Singh gave the "not guilty" verdict here.
"After considering the evidence on record and the observations made by the confirming authority, the court adhered to its original findings and found the accused not guilty of intent to defraud," prosecution counsel Raghavendra Jha told PTI.
The Presiding Officer said there were no new issue to be deliberated and there was no need to interfere in the earlier findings.
The Eastern Army Commander had earlier directed the General Court Martial to reconsider the first charge of "intent to defraud" against Rath when he had been acquitted.
Eastern Command GOC-in-C Lt Gen Bikram Singh had contended that the court, while appreciating the evidence on record, did not accord due weightage and consideration to certain aspects.
"Finding of `not guilty` with reference to the first charge (intent to defraud) appears to be perverse," he had said.
Rath, former Deputy Chief of Army Staff-designate, was the Commander of the 33 Corps when the scam took place in 2008.
The GCM had on January 22 awarded sentence of a two-year loss of seniority and a 15-year pension loss to Rath after he was found guilty on three counts for conveying NoC in the capacity of 33 Corps Commander to a private realtor for constructing educational institutions on a plot adjacent to the Sukna military station near Siliguri in West Bengal.
Rath had questioned the revision order alleging that the "authorities were forcing the court to take a decision in the manner it likes".