Defeat at Eden Park has left the Highlanders' Super Rugby Pacific playoff hopes precariously placed.
Needing victory to clinch their quarter-final spot next week, the southerners were unable to make a dent on the hometown Blues, falling 16-9 in their final regular season outing.
They now face a nervous weekend, with the Force, Fijian Drua and Rebels all capable of depriving them a post-season appointment with the Chiefs.
The Blues won't take much comfort from the result, after leading 16-6 at halftime, but held scoreless over the final 40 minutes by dogged Highlanders defence - especially at scrumtime.
The visitors drew within a converted try in the dying minutes and had a chance to force extra time, with a penalty on their own line and time up on the clock.
Fullback Mitch Hunt found touch outside their 22 and No.8 Hugh Renton won the lineout, but a loose pass from halfback Folau Fakatava put them under pressure and the Blues secured victory with a penalty at the breakdown.
They had a chance to turn the screws and deprive their rivals even a bonus point, but simply kicked for touch instead to end the contest.
"We gave it our best, we gave a lot of heart," said Highlanders captain Billy Harmon. "We put ourselves in a good position, but couldn't finish off."
After an initial exchange of penalties, Blues lock Patrick Tuipulotu scored the only try of the contest, when his pack drove towards the line and flanker Tom Robinson ran a decoy that opened up a wide gap that opened up the defence.
The home side had two other tries disallowed. Hooker Ricky Ricctelli was deprived in the first half, when match officials found a knockon in the build-up, while winger Mark Telea missed out in the second half, when second-five Harry Plummer was dragged into touch.
Second-five Sam Gilbert had a try called back for the Highlanders, when he was found to have knocked on in his pursuit of Jona Nareki's kick ahead.
The Blues had ample opportunity to pad the scoreline, spending much of the second half camped in the Highlanders 22, but could not convert scrum after scrum into points.
"We've got some world class props and so do they, so it was an awesome battle," said Harmon. "Not sure what was going down there, not sure what the refs saw, but that's the scrum.
"We showed some heart there, we battled and it was a massive fight."
Highlanders veteran Aaron Smith likely played his last game at Eden Park, with no All Blacks fixtures scheduled there this year and his imminent departure for Japan after the Rugby World Cup.
Their bonus point does little to help the Highlanders cause, drawing them level with the Reds in seventh on the table, but with a healthy countback disadvantage and three teams still within striking distance.
The Rebels face the Brumbies at Canberra later on Friday. Only three points behind, the Melbourne side also hold a big countback advantage over the Highlanders and would move ahead with any kind of win.
Victory ensures the Blues will host a home quarter-final - probably against the Waratahs - next weekend, but the Crusaders are now secure in the top two and a possible home semi.
Blues 16 (Tuipulotu try; Plummer 3 penalties & conversion) Highlanders 9 (Gilbert 3 penalties)
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