After playing on for 10 minutes beyond the final hooter, the Blues left the field as 32-20 victors and Highlanders head home still searching for a way to win this season.
Covid-19 cases impacted on who was available to take the park on Friday, with the Highlanders leaving some of their squad in Dunedin and the Blues forced into making late changes to the starting side.
Beauden Barrett was in line to make his first appearance of the season for the Blues, but was ruled out. Barrett was replaced at first-five by Stephen Perofeta, after Harry Plummer was already sidelined with a season-ending shoulder injury.
The two sides traded penalty goals early before the Highlanders took a 6-3 lead in the 24th minute.
The Highlanders were awarded a penalty try in the 28th minute to further extend the lead as the Blues were reduced to 14-men for 10 minutes.
At half-time the Highlanders were in control with a 13-3 margin. But that is where the southern side's momentum stopped.
The Blues struck first after the break with back-to-back tries for Taine Plumtree to take a 17-13 lead 10 minutes into the second half.
Struggling at lineouts the Highlanders gifted the Blues opportunities to attack and they eventually made the most of it with a try for Rieko Ioane.
With less than 10 minutes to play, the Highlanders started to edge towards the try line and cause the Blues flashbacks of previous weeks' late collapses.
Shannon Frizell scored for the Highlanders and closed in on the host's score but Perofeta regained the home side's advantage with a try of his own.
The 80 minute mark came and went as both sides bumbled and had moments of brilliance as they held on to fight for different things.
There were disallowed tries, turnovers and tired legs as the Blues were eager to cap off the win with a bonus point in what could be a tightly contested Super Rugby competition, whereas the Highlanders were desperate to add some more credibility to their campaign.
The teams were playing for the Gordon Hunter Memorial trophy.
Hunter was the Highlander's inaugural coach in 1996 after building a strong reputation coaching Otago and following a move to Auckland in early 2000, he became the Blues coach for that year.
Hunter died in 2002 after a battle with cancer.
The two teams have been competing for the trophy since 2002 and it is played for at a home game of the current holder.
The trophy is now evenly shared between the two sides over the past two decades with 10 wins each.