The High Court set aside the 2019 conviction by a special CBI court that had sentenced Ram Rahim and three others to life imprisonment.
Chhatrapati, editor of the newspaper Poora Sach, was shot outside his house in Sirsa in October 2002.
Despite the acquittal, Ram Rahim continues to remain in Sunaria jail in Rohtak as he is serving a 20-year sentence after being convicted in 2017 for raping two disciples.