16-year-old Dheeraj Vishkarma was allegedly abducted when he was standing outside his house, police said, adding that a case in this connection was filed yesterday.
Mr Dheeraj is the son of Ramshankar Vishkarma, witness in the murder of Kripal Singh, who was shot dead on July 10, 2015.
Meanwhile, the boy is said to have returned home, giving a slip to his alleged captors who had taken him to Meerut.
His father Ramashankar Vishkarma had appeared before a court here as a witness on June 7 in the murder case but his statement could not be recorded and has now been called to the court again on June 28.
Mr Ramashankar feared that his son was abducted to pressure him not to depose against Asaram's aides.
The father and brother of the rape victim are also witnesses in the murder case.
Mr Dheeraj said it was when his kidnappers had left him in the car to make some purchases that he fled to the Meerut railway station where the GRP personnel put him in a train to Shahjahanpur and he reached home.
SP City Dinesh Tripathi said that after registering an abduction case, the police went to Vishkarma's house for making some inquiries and found the victim at home.
"The matter is being investigated," the SP added.
On April 24, the self-styled godman Asaram Bapu was sentenced to life-long jail term by a special POCSO court for raping a teenage girl nearly five years ago in his ashram near Jodhpur.