Malhotra defeated Rao by a margin of 72-20 in the elections held here, extending the acting IOA President's long rein in the office which dates back to 1973.
Prior to today, Malhotra has always been elected unopposed as president.
Rao, a former IAS and UN official and now Clean Sports India convener, had accused Malhotra of trying to bring in people who have nothing to do with archery.
The electoral college, which has been declared by Returning Officer Justice (Retd) J D Kapoor under Delhi High Court orders, has 102 members with each state unit getting three votes and each organisation/sports boards one vote.
The AAI election has been mired in controversy as it was postponed thrice after the Delhi High Court directed the returning officer to declare the electoral college amid allegations of manipulation against Malhotra.
The electoral college now includes three North Eastern states -- Arunachal Pradesh, Mizoram and Tripura -- who were not given voting rights by AAI earlier.
A case is still pending in the Delhi High Court on a petition by lawyer Rahul Mehra, praying the court to direct the AAI to conduct the polls under the National Sports Development Code, which has age and tenure restriction provisions.