Hughes went into the break unbeaten on 82 off 161 balls, his innings highlighted by a big six off Rangana Herath, even if the shot - less than cleanly struck - was not one of his best.
Together with Shane Watson, Hughes had helped Australia rebuild after the needless loss of the impressive David Warner immediately before lunch.
Warner, who had 57 of the 97 runs the hosts scored in the morning, was run out trying to grab a quick single that simply was not there, Angelo Mathews picking him off with an easy throw to the non-striker's end.
That ended a strong partnership with Hughes, built after opener Ed Cowan suffered another early dismissal, departing for just four after attempting a pull shot but getting under it to give Shaminda Eranga an easy catch at mid-on.
Watson went late in the second session, caught by outgoing Sri Lanka skipper Mahela Jayawardene off Chanaka Welegedara for 30, with Australia captain Michael Clarke making an unbeaten 7 before tea.
Welegedara had both wickets for Sri Lanka, but they came at a cost as he proved the most expensive of the bowling attack, conceding 70 runs off his 14 overs.