Chief Minister Oommen Chandy said the results were "unexpected" and a "setback" for Congress-led UDF.
Senior BJP leader and former Union Minister O Rajagopal won from Nemom constituency in Thiruvananthapuram by a margin of 8671 votes, defeating sitting CPI(M)-LDF MLA V Sivankutty.
By this victory, Rajagopal has scripted history as all of BJP's earlier attempts earlier to open its account in the state had failed.
However, BJP state president, Kummanam Rajasekharan, former president V Muraleedharan, cricketer Sreesanth and senior leader K Surendran were all defeated.
UDF has secured only 43 seats and Chandy has already conceded defeat, saying the results were unexpected.
LDF's chief ministerial aspirants Pinarayi Vijayan and 93-year-old V S Achuthanandan sailed comfortably to the finish line from Dharmadam and Malampuzha respectively.
Chandy, Home Minister Ramesh Chennithala, Industries Minister P K Kunhalikutty, Revenue Minister Adoor Prakash, Food Minister, Anoop Jacob, Social Welfare Minister M K Munner, Former Finance minister, K M Mani, were among the winners in the UDF camp.
Speaker N Shakthan and Deputy Speaker Palode Ravi were also defeated.
In the LDF, Sebastian Paul and Nikesh Kumar were among those who tasted defeat.
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