Meanwhile, police in Coimbatore district denied permission for the actor to undertake campaign for the Sulur by-poll on Friday.
No one was injured in the incident at Aravakurichi which happened when Haasan was getting off the stage after completing his address. He was escorted to safety, police said.
MNM workers roughed up the two persons suspected to have hurled stones and eggs, before police rescued them and took them away for questioning.
MNM workers staged a protest but police officials held talks with them.
The attack by eggs and stones comes just a day after a slipper was hurled towards a vehicle from which Haasan was addressing an election meeting in the Tirupparankundram Assembly constituency in Tamil Nadu on Wednesday evening.
Haasan, founder of new political outfit Makkal Needhi Maiam (MNM), kicked up a controversy this week with his comment that "free India's first extremist was a Hindu", a reference to Mahatma Gandhi's assassin Nathuram Godse
Police said permission has not been granted for Haasan to undertake the bypoll campaign in Sulur in Coimbatore in the backdrop of the ongoing controversy.
Reacting to the incident Haasan said: "I feel the quality of polity is going down, however, I don't feel threatened".
On his remark on Nathuram Godse he said: "Every religion has their own terrorist, we cannot claim that we are sanctimonious. History shows that all religions have their extremists."
" I am not afraid of being arrested. Let them arrest me. If they do that it will only create more problems. It is not a warning but only an advice," he said.
(inputs from agencies)