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The 24-year-old pipped fellow finalists Sachin Baby and Sidhartha Babu for the honour.
Those who missed out on the final three spots are cricketer Minnu Mani, athlete Muhammad Ajmal, and footballer K P Rahul.
In the recently concluded 2023-24 Ranji Trophy season, the left-hander finished second in the list of top run-getters.
Tamil Nadu captain and left-arm spinner R Sai Kishore was the top wicket-taker with 53 scalps from nine matches.
The sportsperson with maximum number of votes will receive the Manorama Sports Star 2023 award and a cash prize of Rs 5 lakh.
Kerala declared on 514/7 in the final session in reply to Andhra's 272. The hosts were struggling at 19/1 in their second innings at stumps on the penultimate day of the contest.
Vaisakh and Thampi clamied two wickets each for Kerala.
The 35-year-old also went past the tally of 5,000 first-class runs during the course of his knock.
Kerala have just eight points from five matches and their hopes of qualifying for the quarterfinals are almost over.
Kerala fought back to reach 219/4 on the opening day of their Elite Group B match against Chhattisgarh.