Perera fell to the last ball of the day, with the umpires once again forced to call a premature halt to proceedings following a downpour at the picturesque ground on the outskirts of Kandy.
Australia were all out for 203 in reply to Sri Lanka's first innings total of 117, with spinner Lakshan Sandakan taking four wickets on his debut.
The early loss of Perera on the second day of the first Test was another bitter blow for the struggling hosts.
The downpour initially prompted the umpires to call an early tea break, but they were later forced to abandon play early for the second day running.
Veteran Sri Lankan left-arm spinner Rangana Herath and the 25-year-old rookie Sandakan had earlier taken four wickets apiece as the Australian batsman also struggled to cope with a turning pitch.
Adam Voges top-scored for the Australians with 47, meaning no player from either side managed to score a half-century in the first innings.
The 38-year-old Herath, who has hinted that he may soon retire from Test cricket, was the pick of the bowlers and was unlucky not to record a five-wicket haul.
He dismissed both overnight batsmen -- skipper Steve Smith and Usman Khawaja -- in successive overs and had a third wicket in the morning session when wicketkeeper Peter Nevill was caught at mid-on.
After lunch, wicketkeeper Perera dropped a chance off Josh Hazlewood, denying Herath what would have been his 24th five-wicket haul.
While Herath was providing captain Angelo Mathews both the attacking and containing options, Sandakan ran through the lower order to finish with four for 58.
Seamer Nuwan Pradeep finished with two wickets, including that of the resolute Voges who was brilliantly caught by Kusal Mendis at gully.
Voges, who faced 115 deliveries and hit three fours, added 60 for the fifth wicket with Mitchell Marsh, who was among Sandakan's victims.
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