The Crusaders scored their fourth try after the fulltime hooter to clinch the bonus point and comprehensive win.
The score rather blew out as the Crusaders made the most of their numerical advantage, and Carter rubbed salt into the wound with a try near the end.
Nonu was sent off for a dangerous tip tackle on Crusaders winger Tom Marshall in the 57th minute, and the writing was on the wall for a Crusaders victory.
Centre Tamati Ellison said the Highlanders had not played badly but simply did not take the opportunities when they came along.
''I think we had a few more chances and if we had finished we would have been right in there. You just have to take them. These guys are champions, who play for 80 minutes,'' Ellison said.
''We just made mistakes in general. We knew we had to play. You have to mix it up and try and break them into pieces. As a team, if you don't do enough then they are just a better side at playing that sort of rugby.''
Ellison said he was not too down when Nonu was ordered from the field, and felt sorry for his midfield colleague, who he felt got caught by two players going into the tackle.
Both sides showed signs of rust coming off the international break, although the Highlanders came out of the blocks well.
''In that first 20 minutes we definitely played some decent footy and even in the end, when we were down, we made some serious inroads. So we have to be happy with that.
''Penalties can keep you in the game and the funny thing is in rugby that you feel as though you have some momentum but the scoreboard keeps ticking over for them. All of sudden they score a try, plus a couple of kicks and that is the difference.''
It was Ellison's last game in Dunedin as he is off to Japan to link up with the Ricoh club again.
The impressive centre set up the first try of the game after just six minutes when he drew two defenders and threw a no-look pass to Ben Smith.
The Highlanders then kept the Crusaders out for a 10-minute period in the middle of the first half as the visitors camped on their line. They lost Jarrad Hoeata to a yellow card after he raked his hands across the face of a Crusaders forward.
Carter, who slotted eight goals from eight attempts, set up George Whitelock for a try on the half-hour mark for the Crusaders to go into a lead they would never lose.
Andy Ellis scored early in the second half after returning All Black Tony Woodcock missed a tackle in close.
Hosea Gear then got the Highlanders back in the game with a well-balanced try in his 100th game at this level. But right after that, Nonu did his deed and the game was all over.
Carter was the star of the night and Sam Whitelock showed his class in the Crusaders engine room.
Elliot Dixon made a decent fist of playing out of position at openside flanker and Brad Thorn got round the paddock.
Highlanders v Crusaders
The scores
Crusaders 40
George Whitelock, Andy Ellis, Dan Carter, Telusa Veainu tries; Carter 4 con, 4 pen
Highlanders 12
Ben Smith, Hosea Gear tries; Colin Slade con
Halftime: Crusaders 13-7.
Crowd: 18,463
