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The hosts scored 10 points in the final five minutes to claim a 33-26 win at Eden Park.
It was their first win against a New Zealand opponent since 2016.
The Highlanders led 26-23 heading into the final period of the game, before Waisake Naholo was yellow carded for a tip-tackle with 12 minutes to play.
That left the visitors to scramble and while they initially held the Blues out, eventually the defence broke.
The hosts held the ball for 19 phases, showing their threat both out wide and in the tight before Patrick Tuipulotu crashed over to score.
Otere Black followed that up with a conversion and a penalty to secure the win.
The Blues led 15-13 at halftime, their danger from long-range evident.
Twice they showed their threat in the open and left the Highlanders defence unable to cover.
First winger Rieko Ioane hit the line and slipped through the gap between the lineout and first five-eighth.
The Highlanders scrambled, but Ioane was able to get around the cover from Waisake Naholo and went on to score.
That took things to 5-3, before the Highlanders struck back.
A handful of phases later the Blues conceded a penalty under the posts and the Highlanders opted to scrum and keep the pressure on.
That was a good decision, as it demolished the Blues' scrum, Luke Whitelock scoring a pushover to give the Highlanders back the lead.
Again it was another long-range effort which put the hosts back in front.
This time Melani Nanai stepped Liam Coltman as the Highlanders defence scrambled after Akira Ioane snaffled a breakdown turnover.
Nanai's break left him to link with TJ Faiane, who found Rieko Ioane for his second try.
The teams exchanged penalties to open the second half, before Tevita Li pulled in a botched cross kick from Harry Plummer and scored for the Highlanders.
Nanai hit straight back for the Blues though, finishing a break from Faiane to take the score to 23-23.
Waisake Naholo was yellow carded 12 minutes from the end after a tip-tackle on Blues flanker Tom Robinson.
From that penalty the Blues kicked to the corner, but the Highlanders stifled their drive and then won a scrum penalty to clear.
However, the Blues bounced back, going through 19 phases before Tuipulotu crashed over to score the match-winner.
Before play began, the teams linked arms in a circle in honour of the 50 people killed in the attacks on two Christchurch mosques a week ago and a minute's silence was held.