Hughes was the only batsmen to fall in the final session, lasting only a couple of overs after lunch before being bowled through the gate by Chanaka Welegedera, giving the Sri Lankan seamer his third wicket of the day.
Clarke, who had made 70 not out, and Hussey, unbeaten on 37, batted through the remainder of the day and if the evidence of their prolific partnerships in the recent series against South Africa is anything to go by, will take some shifting.
Sri Lanka's bowlers, dubbed this week as the worst pace attack ever to tour Australia by former test bowler Rodney Hogg, made life uncomfortable for the batsmen at times but struggled for any real penetration under cloudy skies at Bellerive Oval.
Clarke, who passed 1,400 runs for the year, has now put on 731 runs in partnerships with Hussey in the last four tests and will be looking to plunder a few more on Saturday despite taking a knock to his ankle.
Friday, however, belonged to Hughes.
The lefthander was recalled to the side on the back of good domestic form following the retirement of Ricky Ponting at the end of the series against the Proteas.
The 24-year-old reached his fourth test half century with a square drive for three runs and then initially accelerated towards a century, most notably with an ugly but effective slog for six off spinner Rangana Herath.
On the ground where his second spell as a test batsman ended amid questions about his technique after two failures against New Zealand last year, Hughes scored eight fours and one six in his 166-ball knock before Welegedera struck with a superb ball.
Australia had lost openers Ed Cowan (four) and David Warner in the opening session, the latter run out for 57 on the stroke of lunch after a calamitous misunderstanding with Hughes.
Shane Watson, dropping down to fourth in the batting order to allow Hughes to come in at number three, followed them to the pavilion for 30 shortly before tea, the victim of an exceptional diving catch in the slips by skipper Mahela Jayawardene.
That was a second wicket for Welegedera and a measure of redemption for the bowler after he had Hughes caught behind for 77 only for the umpire to call a no ball.
Welegedera had also made the early breakthrough for the tourists when Cowan tried to pull a short delivery only for the ball to catch him high on the bat and carry to mid-on where Shaminda Eranga took a simple catch.
It could have been even better for the Sri Lankans, who were only centimetres away from the perfect start to the morning after Clarke had won the toss and elected to bat.
Cowan edged the second delivery of the day from Nuwan Kulasekara to the slips but Angelo Mathews was just unable to get his hands to it, despite an athletic dive.
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