Left-arm spinner Rangana Herath was the pick of the Sri Lanka bowlers, dismissing Australia opener Shane Watson with his first delivery, skipper Michael Clarke and the in-form Ricky Ponting for 44.
Hussey, who came in following the dismissal of Clarke with the total on 91 for three, fell five runs short of his 14th test century, lbw to Sri Lanka captain Tillakaratne Dilshan.
The experienced left-hander had survived a let-off on 76 when Chanaka Welagedara at long off caught him off spinner Suraj Randiv but touched the boundary rope.
"I am disappointed for sure. I would have love to get the three figures," Hussey told a news conference. "But you can look at the other way when I thought I was caught on the boundary at around 80 as well."
"I was just trying to focus on the things that I knew. It does get easier the longer you stay in," he said.
"We have got a good score on the board but it will depend on how well we bowl tomorrow. The wicket got bit of reverse swing. It took a lot of turn on the first day. It was really slow and it was hard to find timing initially."
Ponting, the only other batsman to pass 30, and Clarke added 55 runs for the third wicket before the latter fell lbw to Herath following a decision review.
"It is a wicket you can bat on if you have patience," Herath said. "If we can bat without giving away wickets, that's the best thing we can do against Australia," he said.
Ponting looked in good touch but was caught by Anjelo Mathews at long-off for 44 as he tried to hit Herath over the top.
Usman Khawaja, who scored a century in a warm-up game, was beautifully bowled by fast bowler Chanaka Welagedara just before tea to leave Australia on 157 for five at the interval.
Earlier, opener Watson swatted four boundaries in one over off Welagedara but Herath managed to extract some immediate turn to secure an early breakthrough.
The opener, on 22, tried to push forward but was deceived by the spin and edged the ball to wicketkeeper Prasanna Jayawardene, ending a rapid opening partnership of 28 from six overs.
Paceman Suranga Lakmal then removed Phillip Hughes for 12 after the opener edged a high bouncing delivery to Tharanga Paranavitana in the slips to leave Australia struggling on 36 for two.
Clarke had earlier won the toss opted to bat on a pitch that has historically favoured spin, especially on the fourth and fifth days.
