Bryn Gatland's late drop goal had seen the Highlanders defeat the Chiefs, coached by his dad Warren, in their opening fixture but after a bye week, they were unable to repeat the feat in Auckland.
Mitchell Hunt missed a 73rd-minute penalty and then a drop goal as he failed to tie things up for Aaron Mauger's side, who could not make the most of late pressure in the Blues' 22.
Tries arrived in the opening 11 minutes from the Blues' Caleb Clarke, whose grandfather passed away hours prior to kick-off, and the Highlanders' Ash Dixon.
Scott Gregory's kick was then charged down by Hoskins Sotutu and Dalton Papalii took advantage to cross.
Rieko Ioane made it 22-10 to the Blues before half-time but the same player was sent to the sin bin after the break for an offside infringement. Shannon Frizell added to an impressive try from Hunt to give the Highlanders the lead.
Papalii put the hosts back in front in the 58th minute and Hunt's late miss from the tee spared James Parsons' blushes after he lost the ball while attempting to dive over the ruck to score.
The Blues held firm with some excellent defence, particularly from Sotutu at a late Highlanders line-out, to ensure they retained their 100 per cent record.