The three tries to two win was a gutsy effort from the home side, but the visiting Highlanders now sit winless after three games.
The Hurricanes were strong on defence in Wellington and their bench players made an impact when they came on the field.
Both teams made plenty of errors, but the Hurricanes endured for their second straight win, after last week beating the Blues in a stunning finish.
Hurricanes captain Ardie Savea said Covid-19 was going through the team.
"With omicron, there were some late changes," Savea said.
"One of our guys drove down from Palmy and jumped on the bench and then made his debut."
"I'm really proud of the way the guys came through."
Hurricanes lock Caleb Delaney was one of a number of young players getting a chance to step up. While replacement halfback Logan Henry, from Palmerston North, joined the team as cover and went on to score on debut.
Highlanders coach Tony Brown said the individual performances were acceptable within the Highlanders but the team wasn't working as a unit.
He said that was a concern and rued the missed opportunities.
"We had plenty of possession and plenty of territory, but we couldn't get over the line," Brown said.
"Our leaders have got to step-up next week and create some belief."
"We've just got to start hanging onto the ball and scoring tries when they are available."