Three others, who were close aides of the sect chief, were also convicted by the court.
Krishan Lal, Kuldeep and Nirmal, who were present in the court, were immediately taken into custody by the police and shifted to the Ambala jail.
“All the four accused have been convicted,” CBI counsel HPS Verma told PTI after special CBI Judge Jagdeep Singh pronounced the verdict here.
The judgment was pronounced by the Central Bureau of Investigation (CBI) court judge Jagdeep Singh in Panchkula, adjoining Chandigarh.
Ram Rahim appeared before the court through video conferencing from the Sunaria prison near Rohtak in view of security concerns raised by the Haryana Police and the government.
The quantum of punishment will be pronounced on January 17.
Gurmeet Ram Rahim Singh is currently serving a 20-year prison term in jail for raping two of his followers.
Chhatrapati was shot in October 2002 outside his house after his newspaper 'Poora Sach' published an anonymous letter narrating how women were being sexually exploited by Gurmeet Ram Rahim Singh at the Dera headquarters in Sirsa.
The case was registered in 2003 and handed over to the CBI in 2006.
Khatta Singh, a former driver of the controversial sect chief, had earlier told the court that Ram Rahim had ordered the killing of the journalist.
Ram Rahim was named the main conspirator in the case.
Ram Rahim's conviction had led to violence in Panchkula and Sirsa in Haryana, leaving 41 people dead and over 260 injured.
Besides the Chhtarapati murder case, the sect chief is facing another murder case of former Dera manager Ranjit Singh. The matter is being heard by the CBI court.
(With inputs from IANS)