Sujeesh and Surya were friends for a long time. However, both fell out over some issue, which eventually led to the murder, said police upon preliminary investigation.
Three other accused are absconding. The activists have been booked under non-bailable sections.
The arrested are T Amal, 23, and M V Akhil, 25, both members of the Payyanur North regional committee of the DYFI.
Thiruvanchoor Radhakrishnan MLA was among the protestors as police used tear gas and lathi-charge to disperse the mob after a DySp was injured in stone-pelting, according to TV reports.
Congress party workers have taken to streets protesting SFI's attack on Rahul Gandhi's office in Wayanad.
Jishnu Raj, belonging to Dalit community, was attacked allegedly by activists of the SDPI and the IUML in the wee hours, accusing him of destroying their parties' flex boards.
'It is the responsibility of the LDF to sustain peace in Kerala,' said the CPM leader.
The Congress has announced that it will observe Tuesday as a black day in the State.
Changanassery native Laya Maria Jaison recently made history by earning a place in DYFI State Committee, while Nadira Mehrin from Thiruvananthapuram was chosen vice president of AISF a month ago.
Joisna Mary Joseph, whose marriage with a Muslim man has triggered a controversy in Kerala, appeared before the court on Tuesday morning.