In a free-flowing game the Highlanders were on the scoreboard first with a penalty in the fifth minute, before Devan Flanders scored the first of the Hurricanes six tries.
Both teams were down to 14 men in the 15th minute when Hurricanes captain Dane Coles and Highlanders first five-eighth Mitch Hunt were yellow carded for foul play.
The Highlanders adjusted quickest, with Japanese loose forward Kazuko Himeno breaking away to set up Josh Dickson to score the visitors first try.
While Hunt was off the field, wing Sam Gilbert, who was making return after a nine-month injury lay-off, slotted in to run the play for the Highlanders and took over the kicking duties.
With both teams restored to 15 men, the Highlanders extended their lead with a try for Jona Nareki.
Following a bit of niggle, and an unsuccessful captain's challenge for the Highlanders - which questioned Coles' actions off the ball - Coles crashed over for the home side's second try just prior to halftime.
The Highlanders held a 17-12 advantage at the break but the Hurricanes were back in front less than two minutes into the second half when Ngani Laumape crossed the try line which shifted the momentum.
A successful captain's challenge for Coles helped the Hurricanes hold the lead when a Highlanders try was overturned.
The home side then added another through Du'Plessis Kirifi before the try tit-for-tat continued when Highlanders co-captain Ash Dixon scored in the corner to keep his side in the game.
However, tries to Braydon lose and Salesi Rayasi sealed the second win of the season for the Hurricanes - and their first home win of the campaign.
The four points were not enough to move the Hurricanes off the bottom of the standings. The Highlanders finished fourth in the five-team competition with three wins from eight matches.
Both teams now turn their attention to the Super Rugby Trans-Tasman competition which starts on 14 May.