Patrick Tuipulotu dived over from close range to push the Blues ahead 31-24 in the 71st minute of the Eden Park season opener, but a possible ruck infringement during the lead-up might mean the visitors were hard done by.
Blues prop Charlie Faumuina cleaned out Highlanders outside back substitute Matt Faddes (watch 1:31 in highlights above), who did not appear to be a part of the ruck, helping to clear the way for his side to drive over for their third crucial five-pointer.
If Faddes was not involved in the ruck, then Faumuina should not have initiated contact with him, and the controversial try should not have been awarded.
The incident was one of several decisions that went against the Highlanders and followed the questionable sin-binning of wing Patrick Osborne due to regular infringing.
Highlanders co-captain Ben Smith said his side lacked composure and allowed themselves to be frustrated by referee Glen Jackson's rulings.
"We' were just a wee bit frustrated at times and you just can't get like that in Super Rugby because refs are going to make calls that you don't agree with but you've just got to get on with the game," Smith told Radio Sport.
"And I don't think we did that that well tonight so as a team we're going to have to address that and just look at moving on and playing everything as it is and also adjusting to the ref.
"But the Blues played better than us tonight and deserved the win."
The reigning champions pushed hard in the final stages and managed to narrow the gap with Smith scoring his second try in the 77th minute but the result proved beyond them.