In a series of tweets, Shah blamed supporters of the winning front for the killing and said a committee of party leaders will visit the state to probe the incident.
"I am deeply anguished to learn about merciless killing of our karyakarta (worker) Pramod. This act by supporters of the ruling Left violates the democratic spirit and mandate that the people of Kerala gave them just two days back.
BJP has been targeting the Left over the alleged attacks on its workers in Kerala in the run up to the polls.
Shah had even declined to congratulate the LDF over its win in Kerala, saying it would hurt the "sentiments" of his party workers.
Pramod (38) had sustained head injuries after he was allegedly hit by a brick following a clash during a victory rally by CPI(M) workers at Idavilangu on Thursday. He died the next day.