Tillakaratne Dilshan's century and Hilfenhaus' injury helped Sri Lanka stage a fightback yesterday.
Sri Lanka resumed on 4-87 and were bowled out for 336 after tea on day three in reply to Australia's first innings of 450 for 5 declared as Siddle gave a heroic performance to claim 5-54.
Siddle - who bowled himself to the point of exhaustion when Pattinson broke down with a side strain in the Adelaide test against South Africa last month - performed a similar role yesterday and sent down 25.3 overs including 11 maidens.
Dilshan scored 147 and shared a record fifth-wicket stand of 161 with Angelo Mathews (75).
Siddle finally broke through in the sixth over with the second new ball when Mathews was out lbw at 5-248 shortly before tea.
Mitchell Starc then bowled Dilshan to make it 6-289.
The aggressive Dilshan hit 21 fours in his seven-hour knock, posting his 15th test hundred and second against Australia.
Siddle removed Prasanna Jayawardene lbw for 40 on a third-umpire referral.
Rangana Herath was also lbw to Siddle for a duck. Unfortunately for the batsman, TV replays showed an inside edge on to his pad but the tourists had no referrals remaining.
Australian fast bowling casualty ward
Patrick Cummins (back) - aiming for an Ashes tour comeback
James Pattinson (side) - ruled out for the test season
Josh Hazlewood (foot) - another month on the sidelines
Ryan Harris (shoulder) - aborted a Big Bash League return
John Hastings (back) - cleared of serious damage but rested from BBL
Ben Hilfenhaus (side) - unknown
- AAP