After waking up feeling unwell and forgoing the usual pre-match warm-up session, Sinner eventually triumphed 6-3 3-6 6-3 6-2 to set up a quarter-final with either Australian No.1 Alex de Minaur or American Alex Michelsen.
Sinner looked in serious physical distress in the first few games of the pivotal third set on Monday before leaving the arena to receive treatment on the advice of his support staff when leading 3-2.
Jannik Sinner looked refreshed after taking a medical timeout in his win over Holger Rune. (James Ross/AAP PHOTOS)
He returned to Rod Laver Arena a rejuvenated man as the temperature in Melbourne reached 32 degrees - and presumably more in the closed confines of Rod Laver Arena.
Three games later the 13th-seeded Rune called his own timeout for treatment on his right leg, only for Sinner to hold to love in the following game to claim the third set.
There was another halt in proceedings one game into the fourth set while officials repaired the bracket that holds the net in place.
Officials worked hard to repair the net on Rod Laver Arena. (James Ross/AAP PHOTOS)
Sinner stepped up the pace on the resumption and Rune was unable to respond as the Italian broke in the third game and again in the seventh before closing out the match in three hours and 13 minutes.Â
"It was very, very tough," said Sinner in his on-court interivew.
"I knew in my mind that (Rune) also had some very long matches before this one, so I tried to stay in there mentally.
"I just tried to stay connected with my service game and then in the return games, it was trying to see what happens.
"Today the support meant so much to me, so thank you so much.
"I really needed you guys today - so it was 90 per cent yours and 10 per cent me trying to make you happy."
The red-hot No.1 - who won his first two major titles last year at the Australian and US Opens - has only lost two matches since bowing out in the quarter-finals at Wimbledon and is now on an 18-match winning streak.
He and the 21-year-old Rune had split their previous four encounters 2-2, each of which went to a deciding set, and it didn't bode well for Sinner when he woke up feeling unwell on Monday.
"It was a very strange morning because I didn't even warm up today," he said.
"I was just trying to go on court as fit as I could be.
"I knew in my mind already before the match that I would struggle today.
"I would have to say that game-wise I played well."
Rune had been taken to five sets in two of his three previous matches at Melbourne Park.
Holger Rune's run at the Australian Open was ended by Jannik Sinner. (James Ross/AAP PHOTOS)
Lorenzo Sonego ensured there would be two Italian men's quarter-finalists at the Australian Open for only the second time.
Sonego ended the unlikely run of US qualifier Learner Tien, winning 6-3 6-2 3-6 6-1.
It was the first time the 29-year-old Sonego had advanced to the quarters at a major on his 22nd attempt.
