Prabhakar Reddy himself told reporters that he voted for Subbarami Reddy.
Khan polled 49 votes while Subbarami Reddy and Ramachandra Rao got 46 each. TDP nominees bagged 38 votes each while Keshava Rao got 26 first preference votes.
A legislator of the ruling party availed None Of The Above (NOTA) option, introduced for the first time in the history of Rajya Sabha elections while another lawmaker dropped a blank ballot paper in the ballot box.
Assembly Speaker N. Manohar, Chief Minister N. Kiran Kumar Reddy and TDP chief N. Chandrababu Naidu were among the first to cast their votes.
YSR Congress party's 23 legislators, Bharatiya Janata Party's (BJP) four members and the lone lawmaker of the Communist Party of India-Marxist stayed away from the voting.
The Telangana issue overshadowed the polls with the Congress legislators from Telangana voting for the candidates from the region. They said they would cast their first preference vote to party candidate Khan and the second preference vote to Keshava Rao.
The TRS general secretary was also backed by Majlis-e-Ittehadul Muslimeen (MIM) and Communist Party of India (CPI).
Out of the six seats which fell vacant, five were held by Congress and one by the TDP.