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With two minutes on the clock, the Hurricanes were in position to launch an attack, but Berry called a knock on against Perenara to put an end to their hopes as the Crusaders took out the match 30-26.
Replays appeared to show Crusaders lock Sam Whitelock had reached over the breakdown and illegally swiped the ball from Perenara's grasp.
A deflated Perenara said the Hurricanes should have been awarded a penalty. Instead the Crusaders were rewarded with a scrum feed inside their own quarter, before clearing for touch on the fulltime hooter to win the pulsating game.
If the Hurricanes had been awarded a penalty they would have had one last chance to attempt to score a try to claim a victory and advance to the final.
"We know it's a penalty," Perenara said. "The ref can't see everything. He makes a call, and calls it a knock on.
"Sometimes we expect a penalty, there, for a deliberate knock down; but it is what it is in a game of footy."
Hurricanes coach John Plumtree agreed with Perenara.
"I think something happened in that last ruck that you guys (the media) might want to have a look at, at some point," Plumtree said.
Despite the controversial finish, fans were treated to one of the best games of the season - with the Hurricanes putting up a strong challenge right until the final whistle.
In the end, the Crusaders showed how difficult it is to beat them at home.
The hosts broke out to a fast start, going up by three points in as many minutes, before a brilliant cross kick from Ryan Crotty found winger Sevu Reece in the corner for the opening try of the match in the 13th minute.
The Crusaders outran Hurricanes by 100m in the first half, with the Hurricanes making far more tackles. However, the Crusaders kept the door open – with 12 turnovers conceded in the first half.
It was a different story in the second half as the game opened up and both sides played fluid, attacking football.
Ultimately the Crusaders hung on and booked a place in the final against the Jaguares next week.