The win puts the team back in the running in the Super 15 and was built on some grit and effort in the tackle as the Hurricanes tried to tie the game up near the end.
The key period was right at the end, when the Hurricanes pressed on to attack, and camped close to the Highlanders line for the final 10 minutes. But the home team would not buckle.
It was gutsy defence, although the Hurricanes were guilty of being too one-dimensional. They barged repeatedly at the line when Ma'a Nonu, one of the hardest men to stop in world rugby, twiddled his thumbs out in the middle of the backline.
The Highlanders forwards hunted as a pack in those final minutes and though they were squeezed, they never gave in.
It was an exciting last few minutes but the second spell had meandered along as the game was played between the two 22m marks.
Best for the Highlanders was prop and captain Jamie Mackintosh, who ran the ball up time and time again and grabbed a couple of turnovers.
Lock Josh Bekhuis got through plenty of work, while No 8 Nasi Manu made metres every time.
Halfback Jimmy Cowan had an outstanding match, clearing the ball well, making his tackles, and looking composed in everything he did.
Lima Sopoaga was a very mixed bag but banged over an important goal in the second half, while Ben Smith continued to display outstanding form.
The opening 20 minutes of the match was a testing-out period and the Hurricanes looked the more threatening, after Aaron Cruden kicked a simple penalty after two minutes.
But any time the visiting team got going, there was a knock-on or loss of control.
Just after 20 minutes, Hurricanes No 8 Victor Vito ran 50m from a scrum under his own posts. The Hurricanes poured on to attack and after Nonu charged to within a hair's breadth of the line, lock James Broadhurst was denied a try after a long look by third match official Richard Kelly.
The Hurricanes still had an attacking scrum but could not get over and the Highlanders forced a penalty.
Then it was the Highlanders' turn to attack.
Sopoaga had a gilt-edged chance after 30 minutes, with one man to beat, but he passed too early to Cowan and the cover defence got hold of the halfback.
The Highlanders were awarded a penalty from an earlier infringement but Sopoaga missed a kick he probably could have thrown over.
Reward for the Highlanders finally came five minutes from halftime, when they moved the ball to the right and after four rucks, Smith won the race to a clever Cowan chip over the top, charging in front of a couple of Hurricanes defenders to score.
Sopoaga nudged over the difficult conversion.
On the stroke of halftime, the Hurricanes were caught offside after a poor clearing kick by Jayden Hayward, and Sopoaga slotted the penalty from 44m out, straight in front, to give the Highlanders a 10-3 lead.
Both sides traded penalties in the first 10 minutes of the second half but from there, the game became stop-start because of injury stoppages, and neither team could hold on to the ball for long enough to mount any pressure in the wet, greasy conditions.
HIGHLANDERS v HURRICANES
- The scores
• Highlanders 13
Ben Smith try, Lima Sopoaga 2 pen, con
• Hurricanes 6
Aaron Cruden 2 pen
• Halftime: 10-3
• Crowd: 8000
