While SFI's KS Anirudhan managed to garner 892 votes, KSU's S Sreekuttan, who challenged the election in the High Court, got 889 votes.
The High Court had declared the earlier election invalid and ordered repoll.
The protest was against DCP Baiju, who had a KSU worker in a chokehold while taking him into custody for waving black flags at Chief Minister Pinarayi Vijayan recently.
The Kerala High Court had earlier asked how the invalid votes in Kerala Varma College elections increased and NOTA votes decreased during recounting.
One of the students sustained an eye injury.
The court was considering a plea filed by KSU's chairperson candidate S Sreekuttan.
College principal Dr A P Shariff got into an altercation with the KSU activists, who turned up at the college to call for a strike as part of the statewide education bandh on Tuesday.
KSU activists clashed with police during a protest march to Higher Education Minister R Bindhu's official residence.
In the visuals aired on the news channels, a cop was seen hitting the woman protester's face with his lathi.
Court refused to issue an interim order banning the SFI candidate from assuming the post of the college union chairman.