The dropped set against Hurkacz, who replaced the injured Stefanos Tsitsipas in Turin, confirmed Jannik Sinner's spot in the semi-finals - making him the first Italian in the tournament's 54-year history to reach that stage.
Serbian Djokovic will now have to wait for the final group match between Sinner and Denmark's Holger Rune later on Thursday to learn his fate. Djokovic needs Sinner to beat Rune to advance.
Playing with nothing to lose, Poland's Hurkacz was a force to reckon with on serve - firing 24 aces in the match - but he ran out of steam in the final set as Djokovic converted break points for the first time in the contest.
Despite Djokovic notching his 15th victory over a top-10 player this year, equalling his best record since 2018, the Serbian was clearly frustrated after the win when asked why he looked upset when things went awry during the second set.
"Why was I upset? For what? I lost the set, so it's normal... Good win, good win," he said in an interview that lasted less than 20 seconds before he walked off the court.
Break points were in short supply in an absorbing first set as Hurkacz made things difficult for world number one Djokovic when he opted to serve first and began with a series of unreturned serves in the opening games.
Hurkacz is the only player on the ATP Tour with over 1,000 aces in 2023 and the 26-year-old was aggressive with his approach on a lightning-quick surface.
But at 6-5 down, Djokovic switched gears and won 10 points in a row to take the contest into a tiebreak, setting up six set points in the blink of an eye.
Although Hurkacz saved one set point, the Serbian closed out the set to take the upper hand.
However, the Pole stormed back into the match in the second set with the crowd firmly behind the underdog while Djokovic seemed distracted, handing Hurkacz the first break when he made a double fault.
Hurkacz nearly handed back the advantage on serve when leading 4-3 with Djokovic going 40-15 up, but his powerful serve came to the rescue once again to deny the Serbian a break before he served out the set to force a decider.
However, that was all Hurkacz had to offer as his unforced error count continued to climb. Although the Pole hit more winners than Djokovic, he also made 41 unforced errors which proved to be the difference.
