Victory will be all the sweeter for the hosts, who celebrated 100 Super Rugby games for halfback Finlay Christie, and a first for prop Ben Ake on debut.
The Highlanders, meanwhile, left their run too late, with only a late flurry of tries in the final minutes adding credibility to the scoreline, and running out of time to force Super Point.
While they were able to pull the score back from 40-21, it was too little too late for the Highlanders - who remain winless at Eden Park since 2018.
Jamie Joseph’s side were plagued by handling and discipline errors, and were hit hard by the loss of standout winger Caleb Tangitau when he failed a head injury assessment after a high shot from Zarn Sullivan.
The Highlanders remain seventh on the table, but could fall fall further if other results go against them this weekend.
While the Highlanders opened the scoring through the individual brilliance of Adam Lennox, who slipped through a gap from a lineout, the Blues answered with power, as repeated attempts at their opposition’s line finally saw Hoskins Sotutu barge over from close range.
Minutes later, the 0-7 deficit became a 12-7 lead. A linebreak from Dalton Papali’i saw the Blues shift right, before Segner surged over - and held off three tacklers - to score his first, and immediately win a turnover after the restart.
As the first half wore on, the Highlanders were plagued by handling errors and ill-discipline. A knock-on from Tangitau saw the Blues’ lay the platform for a third try, capped off again by a forward crashing over, this time through lock Sam Darry.
Down 19-7, the Highlanders’ answered back - albeit at a huge cost, as a break from Tangitau put the Blues on the back foot, and sent Tanielu Tele’a over in the right corner against his old side.
However, that was the end of Tangitau, after he was hit high Sullivan - who earned a yellow card - and was taken from the field on a medicab as a result. It was only the fact that Tangitau was already falling at the time of the contact that saved Sullivan from his yellow turning into a red, as the Blues reached the break 19-14 ahead.
After halftime, and back at their full complement, the Blues picked up where they left off, as a lineout maul yielded a fourth try, scored by Bradley Slater, before Segner had his second with a clean break to dot down under the posts, and push the scoreline beyond two converted tries.
Needing to score next, Lennox slipped through the Blues’ line again, this time from much closer range, to pull the gap back to 12 points. Hopes of a comeback were derailed minutes later, though, as Cole Forbes went over on the right wing, as the first Blues back to score on the night.
The Highlanders were able to grab three consolation efforts, through substitute Xavier Tito-Harris, a Tele’a second and replacement hooker Soane Vikena, either side of a debut effort from Ake, as AJ Lam was shown yellow for a cynical penalty at the end.
Both sides will head south to Christchurch next week, where the Blues meet the Reds and Highlanders face Moana Pasifika for Super Round at Christchurch’s One New Zealand Stadium.
Blues 47 (Sotutu, Segner 2, Darry, Slater, Forbes, Ake tries, Barrett 6 conversions)
Highlanders 40 (Lennox 2, Tele’a 2, Tito-Harris, Vikena tries, Millar 5 conversions)
HT: 19-14