Recalled on the back of good domestic form after the retirement of Ricky Ponting, the 24-year-old lefthander had reached 82 not out at the break under overcast skies at Bellerive Oval.
Australia 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 to bring skipper Michael Clarke (seven not out) to the crease.
Warner will take the blame for his runout after appearing to set off for the run only to change his mind. Hughes could hardly be criticised for backing up well to leave his partner stranded at the other end.
Hughes resumed on 27 after lunch and moved cautiously towards his fourth half century 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.
He reached the milestone with a square drive for three runs and then initially accelerated towards a fourth Test century, most notably with an ugly but effective slog for six off spinner Rangana Herath.
The Sri Lankan bowlers, described this week as the worst pace attack ever to tour Australia by former Test bowler Rodney Hogg, bowled tidily but without any real penetration.
It was an exceptional piece of fielding from Mahela Jayawardene that led to the dismissal of Watson, the Sri Lanka skipper making a brilliant diving catch in the slips off the bowling of Chanaka Welegedera.
It was a measure of redemption for Welegedera, who had just had Hughes caught behind for 77 only for the umpire to rule a no ball. The call was backed up by television pictures that showed the bowler's front foot well over the line.
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.
The opener faced just 16 further balls before departing with just 18 runs on the board, bringing Hughes to the crease for his third stint in Test cricket.