Murugesan resigned to keep his promise to party supremo G Palanivel that he would resign should he lose in the polls.
He will be succeeded by Sakthivel Alagapan, 43.
In a statement posted on the party website, Murugesan, who lost to opposition PAS in the Kota Raja parliamentary seat, said he had informed Palanivel about his decision last week.
"The party needs to rejuvenate and renew itself. I have given my best as secretary-general to move the party forward and be more relevant to the younger generation," he said.
Meanwhile, Sakthivel expressed his intention to redeem the party's pride by focusing on several core issues.
Sakthivel, who also lost a six-cornered fight to opposition PKR's G Manivannan, said he was happy with his appointment.