WRFU club liaison officer Paul Kenny said the incident happened immediately after the June 25 clash with Ruapehu, who scored a converted try in the dying seconds to win 25-18.
"The [first] judicial hearing was for verbal abuse by Denning, and physical abuse by someone that couldn't be identified," said Kenny.
"The player had been subbed and had put a hoody on."
The Pirates club later identified Vili as the player who grabbed the official's throat, with the judiciary hearing banning him from all rugby until January 1, 2018.
Kenny said it appeared Pirates were initially going to appeal the sentence, but ultimately did not do so, and then the Referees Association did.
A new hearing was convened in front of a different committee, attended by several Pirates including life members.
"There was no additional evidence because the crimes had been committed and admitted to," said Kenny.
"[The hearing] took into account the reasons it should be longer, and stood him down till January 2019.
"They are trying to get uniformity around the country with penalties being on the harsher side.
"The physical touching of a ref is a no-no."
Extending Vili's stand down to nearly three years comes only a week after a Freyberg B player was banned from his club for life after allegedly punching a referee in the back of head just after fulltime in a Manawatu club game.
Referees Association facilitator Neville Hopkins said the grabbing of the official "was totally inappropriate".
"The referee concerns - how can we expect to attract referees or get people to take up refereeing, when something like that happens?
"We've had a big incident in Manawatu last week, and another in Christchurch.
"It's not good for rugby to see that happening.
"Discipline is the responsibility of the players, captains, team management, and ultimately, clubs."
Pirates still have the right to appeal the length of the sentence with the New Zealand Rugby Union.
Kenny said the WRFU opted not to make the punishment public until after the second judiciary hearing.
"We couldn't do anything because it was only appealed last Wednesday.
"The players had to be informed [of the decision] in writing. They were given a verbal on Thursday.
"The report - I didn't receive that until late Friday."
WRFU chief executive Bridget Belsham said they had to make sure the matter was dealt with appropriately, given two different volunteer committees looked at the matter.
"I just wanted to make sure we followed the right process, without outside influences from media or anyone. We didn't want to undermine the decision.
"The referee's had every right to appeal.
"There was no way we're ever going to let someone get away with touching an official."
Pirates president Jeff Slight said the club did not wish to comment on judicial matters at this time.
Pirates still intend to play the Premier consolation final this Saturday against Kaierau at Cooks Gardens.