Hussey was disastrously run-out for 25 in his last Test just minutes after tea and then even captain Michael Clarke was sent packing with his side still trailing the tourists.
Clarke tumbled straight after bringing up his 50 when the form skipper played an uncharacteristic 'slog-sweep' and skied a difficult high catch into the in-field from cagey spinner Rangana Herath.
At stumps Australia had chiselled out a lead of 48 at 6-342 with wicketkeeper Matthew Wade on 47 and Peter Siddle 16, in reply to Sri Lanka's 294.
Sri Lanka, already two-nil down in the three-match series, is well back into this match on the back of a brave battle to prevent the home side building any substantial first innings lead.
Australia heads into the third day precariously placed needing a healthy lead to avoid chasing a difficult last inings score on a pitch expected to deteriorate late on the fourth and fifth days.
No side has ever scored more than 300 in the last innings to win a Test at the SCG.
Signs of variable bounce and occasional puffs of dust lifting from the strip are already alarming late on the second day of the dry pitch.
A belligerent Warner looked certain to complete a run-a-ball century before he was out for 85 to his only real blemish in a sparkling 150 minutes, while Hughes mis-judged a cut-shot from Herath and was out for 87.
Wade, Mitchell Johnson (13) and Siddle were the top of a lengthy Aussie tailend batting make-up after the home nation played four specialist pacement and bowled first in the match on winning the toss on Thursday morning.
Australia's batting was littered with poor decisions that generated two run-outs and surprising shot-selection from Warner and Clarke when well set.
Hughes also chose to cut when the Herath spinner was probably too close to his body and keeping low.
Hussey was caught short diving into his crease after a bungled quick single called by Clarke.
The in-form skipper pushed into the off-side and called Hussey but Dimuth Karunaratne swooped and hit the stumps with his whippy throw from the in-field.
Wade was dropped twice in his cautious stay and given a vital life on 10.
He was turfed in a sharp chance at short-leg from off-spinner Tillakaratne Dilshan and Australia on 4-265, still 29 runs short of Sri Lank's 294.
Warner paid the full price for his only really rash shot when he mis-judged an attempted lofted drive and was caught shortly after lunch and Hughes followed also in the 80s.
Hussey, 37, is making his final Test appearance after announcing his retirement last week.
He averages 100 in his seven previous Tests at the famous SCG, as well as 117.8 against Sri Lanka with five centuries.
Hussey strode to the crease to a rousing reception from an adoring SCG crowd and a respectful guard of honour from the tourists.
Warner smashed his way to a half-century in just over the first hour from only 37 balls, despite an early setback in a poor piece of running between wickets from his opening partner Ed Cowan.
Cowan was run-out at the non-striker's end after ambling his first run when the pair appeared set for a simple two.
Warner was out for the fourth successive time in the three-match series after posting a half-century and not making it through to the magical ton.
The excitement machine put together scores of 57 and 68 in Hobart's First Test and then 62 from only 46 balls in Melbourne.
Warner and Hughes put on an enterprising 130-run stand in only 30 overs for the second wicket after the early loss of Cowan.
In just his 15th Test, Warner went through the 1000-run barrier which includes three centuries since his anticipated debut against New Zealand in December of 2011.
Highlighting the Australian top-order's brisk early run-rate Warner and Hughes deprived Sri Lanka any maidens in the first 20 overs as they posted a century more than 30 minutes before the lunch break.
Ironically, Sri Lanka captain Mayhela Jayawardene opted to use part-time spinner Dilshan to send down seven overs (0-19) ahead of front-lin left-arm orthodox tweaker Herath as the Australia's settled into a potentially big stand.
Herath, 34, has 179 scalps under his belt from 44 Tests and did not bowl a single delivery as the Australians laid foundations for a potentially massive first innings tally.
Herath was injected into the attack immediately after lunch and had instant impact with a devilishly close leg-before-wicket call and review on the dangerous Warner who survived a lenghty video analysis on 70 and the Aussies 1-129.
The wily spin of Dilshan did, though, did bring about Warner's demise in spooning a drive to bowler Dhammika Prasad at deep mid-off.
The home side launched their run chase from the opening delivery of the second morning after dismissing the tourists just before stumps on Thursday.
Australia is understood to have set sights at a target in excess of 500 and probably bat for up to two full days to ensure a small last innings total in any run-chase to win the match on Sunday or Monday and the pitch likely to play awkwardly.
Clarke surprisingly elected to bowl first when he won the toss ahead of play starting and he had four specialist pace bowlers in the his side.
Australia wrapped up a plucky Sri Lanka innings just before 6pm on the opening day of an emotion charged Sydney Test when there was not time left in the session to start the home side's batting.
New seam bowling star Jackson Bird inflicted most pain on Sri Lanka's path-up batting make-up with four scalps (4-41), while strike paceman Mitchell Starc with three (3-71) and reliable speedster Peter Siddle (2-46) and spinner Nathan Lyon with one shared the wickets.