Vision from Eden Park after fulltime in the Knights' 12-10 victory showed Klein being hit with a raft of bottles, cups and rubbish as he walked from the field.
The footage shows Klein having to be protected by security, as fans abused the veteran referee and projectiles rained down on him.
The NRL immediately launched an investigation into potential breaches of their spectators' code of conduct. An Integrity Unit investigator had been at the ground.
"If found guilty, they will be banned for a period of time from attending NRL games," ARL Commission chairman Peter V'landys told AAP.
V'landys' no-nonsense stance was welcomed by the referee's union, Professional Rugby League Match Officials (PRLMO), who called on the NRL to come down hard on the Warriors supporters.
"The safety of all referees and match officials is paramount, and they should be allowed to perform their duties without being placed in harm's way," PRLMO chair John Choueifate told AAP.
"To say I was disappointed is an understatement and call on the NRL to investigate the incident which detracted from an enthralling match.
"They need to send a very clear message to those responsible and to others in future that this rubbish must be stamped out of the game."
New Zealand Police confirmed no arrests were made, with "no issues to note" other than two pitch invaders.
The Warriors did not respond to AAP requests for comment.
Sunday's crowd of 48,511 marked the biggest ever for a rugby league match in New Zealand, after the NRL made the call to move the game from the Warriors' traditional Mt Smart Stadium home.
The NRL's investigation came as they admitted Klein had erred with a crucial decision not to penalise Newcastle prop Tyson Frizell for an escort in the dying minutes.
Had it been awarded, the Warriors could have levelled at 12-12 and sent the game to extra time. It's understood Klein will be dropped for the preliminary finals.
Regardless, Warriors great Shaun Johnson hit out at fans, labelling their behaviour as "embarrassing" and said a missed call was no excuse for that reaction.
"Ashley Klein is a human being in the middle of a park doing one of the toughest jobs there is," Johnson said on his Instagram.
"In what world do we think that is okay? You guys are so quick to point out that athletes and ex-athletes are role models for your kids.
"Well you're not setting the bar very high if that's what they've got to look up to. Be better man.
"It's such a s*** way to finish a season. Not just from a result standpoint. But leaving such a sour taste from a fan base. A fan base I deeply care about."
Warriors coach Andrew Webster had vented his frustration in the post-match press conference, highlighting a bunker strip call on Te Maire Martin and the decision not to penalise Frizell for a possible escort on Leka Halasima.
The incident comes after AFL umpires also had cans thrown at them while leaving the MCG after Hawthorn's tight loss to Brisbane in Saturday night's preliminary final.
The AFL has also condemned the behaviour and warned of minimum five-year bans for any fans found responsible.
