State intelligence officials made the arrest in the early hours of this morning (08) at Maharagama.
The man was identified from footage of CCTV cameras installed near the attacked shops.
He has suffered burn injuries to a leg during the attacks.
Footage shows him arriving at the closed shops in the night and the shops catching fire thereafter.
Under interrogation, he has confessed to having lobbed the petrol bombs at the shops, and investigations are underway to determine as to why he had resorted to such acts.
From 22 May to 06 June, two shops at Maharagama, a pharmacy and a cushion business at Wijerama were badly damaged in arson attacks.
Just yesterday, president Maithripala Sirisena said that he would have to relieve the police from duties over failure to prevent racial and religious clashes.
Meanwhile, police sources say they have received reliable information with regard to the whereabouts of Bodu Bala Sena general secretary Galagodaatte Gnanasara Thera, wanted over hate speech complaints, and that he will be arrested within days.