A Bench headed by Justice P Sathasivam dismissed the plea filed by the family of the victims.
The family had alleged that the ashram authority was involved in the case and it was not possible for the state police to conduct a free and fair investigation.
The Bench after going through all the evidence said there is no need for a CBI probe but clarified the trial court can order further probe, if some new facts come up.
The apex court dismissed the appeal filed by the family challenging a Gujarat High Court order, which too had refused to direct a CBI probe in the case.
Two young boys Deepesh and Abhishek had gone missing from the ashram on July 3, 2008 and two days later on July 5, 2008, they were found dead outside the ashram.
The victims\' parents had filed the writ petition in the high court seeking a CBI probe.