Justice A Muhammed Mustaque admitted the writ petition filed by Raveendran, challenging the order and stayed further proceedings.
Raveendran contended that Lok Ayukta had no jurisdiction to pass an order related to the internal issue of a political party and that it was limited to irregularities of public servants.
The case relates to CPI making Abraham, a non-party worker, its nominee in the last election after allegedly receiving funds from him.
A committee set up by the party that probed the defeat of Abraham had found lapses in his selection as candidate.
CPI had also initiated disciplinary action against three party functionaries in this matter, two of whom recently quit the party.