Despite their attack not flowing, the Hurricanes enjoyed plenty of possession in the second spell and that pressure eventually became too much for the Waratahs to handle.
Barrett's absence meant Fletcher Smith started at No 10, although regular halfback TJ Perenara finished the game playing at first-five, as replacement pivot James Marshall lasted only a few minutes in his return to Super Rugby before he was injured in the second half.
The Waratahs hosted the match at Brookvale Oval - home of the NRL's Manly Sea Eagles - due to the redevelopment of regular stomping ground the Sydney Football Stadium.
Bernard Foley's first penalty of the evening gave the Waratahs a 3-0 lead and made the pivot the highest-scoring Waratahs player in Super Rugby, overtaking Matt Burke who amassed 959 points.
The opening quarter was challenging for the Hurricanes as they were unable to get their discipline under control. They gave away six penalties inside the first 18 minutes, which can't have pleased coach John Plumtree.
The visitors finally got themselves into the game following the 20-minute mark and eventually their ability to hold onto the ball turned into points when Ardie Savea nabbed the game's first try.
The Waratahs took a 12-10 lead to the break courtesy of Foley's boot and extended that advantage in the second spell with a try to Curtis Rona, but neither side was able to assert a great deal of dominance in the game as ill-discipline and poor handling proved an issue.
Jordie Barrett's successful conversion was a difference-maker following Kirifi's try, as Foley sprayed a late penalty attempt that would have won the game for the Waratahs.
Savea was immense throughout the contest for the Hurricanes, while hooker Dane Coles made an industrious return to Super Rugby from the bench for his first appearance in the competition since 2017.
The Hurricanes will be counting the days until Beauden Barrett's return.
Hurricanes 20 (Ardie Savea, Du'Plessis Kirifi tries; Jordie Barrett 2 pen, 2 con)
Waratahs 19 (Curtis Rona try; Bernard Foley 4 pen, con)
Halftime:
10-12