Early morning showers delayed the start of play at the Bellerive Oval by 50 minutes and just 13 balls into the session Shaminda Eranga broke the most prolific partnership in Australian cricket this year.
Clarke had managed to add just four runs to his overnight tally of 70 before a delivery from the young paceman induced the Australian captain into an edge which Kumar Sangakkara collected with ease at second slip.
Hussey, who in the last four tests has put on 736 runs in partnerships with Clarke, had made 66 not out at the end of the opening session with wicketkeeper Matthew Wade unbeaten on 31.
The bad news for Sri Lanka is that Hussey rarely makes a half century without converting to a big score and the 37-year-old had started to open up after reaching 50 with a single to mid-off.
Wade looked less assured, especially with some of his run calling, and he survived an optimistic lbw appeal from Chanaka Welegedera when the TV umpire confirmed the ball had pitched outside the line of the stumps.
There was another scare two overs later when Wade pulled a short delivery from Welegedera and replacement fielder Suraj Randiv just failed to hold a catch at midwicket.
Sri Lanka's bowlers, dubbed by former Australian test player Rodney Hogg as the worst pace attack to tour the country, made life difficult at times for the batsmen and will be disappointed not have made further inroads into the Australian order.
The tourists have never won a test in Australia and will have two more attempts at breaking that duck in further matches in Melbourne and Sydney.