Additional District Judge Ramesh Chandra Diwakar exonerated Ram Ji Verma of all the charges, saying that the 34 witnesses, who testified in the case, "either turned hostile or indifferent or showed ignorance".
The judge said that even the main eyewitness said "he had only heard and not seen anybody pushing Manish out of the train".
One of Manish's friend, Rakesh, who was with him had sustained injuries in the clash.
An FIR was filed in this case by Manish's father, Mahendra Kumar Mishra, and another by Rakesh's brother at GRP Kosi Kalan station.
The prosecution, however, said it would move the high court against the court's order.