The former Indian Administrative Service officer described the BJP's prime ministerial candidate Narendra Modi as a 'good friend' of the Tamil Nadu CM on a television show.
Malaichamy had also said AIADMK would play a vital role in the Modi government after the results are announced.
Watch video: Jayalalithaa suspends party leader over BJP alliance remark
Jayalalithaa, who is yet to disclose her political moves, had said on Wednesday she would reserve her comments until the election results are announced on Friday.
A party statement said Malaichamy has been removed from the primary membership of AIADMK for violating party discipline and for bringing disrepute to its image.
Within minutes of Malaisamy's expulsion, AIADMK leaders clammed up and refused to divulge any information other than insisting "Amma will take a decision after election results are out tomorrow".