Just before the break, Rotoiti had a player sin-binned for a late charge that turned out to be crucial as the Mount scored two tries against 14 players within three minutes of the restart.
Rotoiti slipped off a tackle from mobile tighthead prop Josh Davey, who sprinted upfield and linked well with Marnus Hanley and Malakai Kisina before replacement back Pera Gibbs scored.
From the restart, Rotoiti made the same error and this time it was Te Aute who showed his startling acceleration to outpace the defence and score.
Down 23-8, the Rotorua boys, urged on by a healthy-sized travelling support crew, attacked the Mount line but the decision to take a scrum from a penalty near the line backfired as they were pushed off the ball.
Rotoiti had another drive for the line but turned the ball over.
Veteran Zar Lawrence ran from deep and found Te Aute.
The Steamers utility took off on a mazy run that went 60m before he unselfishly fed Gibbs for the match-winner.
There was time for a late try to Matty Axtens and points from the tee for Golding before excellent referee Jamie Bell whistled an end to the 2017 Premier 1 season.
Mount coach Rodney Voullaire was proud of how his entire squad had improved during the season after a slow start to round one.
"I always knew this team was coming but it was a long wait. We went through 58 players this season and it is a big shout out to our development coach John Beard.
"Today Rotoiti from Rotorua were always going to be tough but hey the weather was good for us today as we love to play width."
Voullaire had special praise for his fullback turned halfback Te Aute, who changed the final with his blistering pace.
"He is a class act. He didn't make NZ Sevens for nothing or the Bay for nothing. Nine is a great position for him and I hope he sticks to it. A bit more time there and he is going to be very dangerous."
Rotoiti coach Richard Francis was gracious in defeat.
"It was not a thrashing and the boys put everything into that game but we made some basic errors at the wrong time. They let us down at the end of the day," he said.
"The sin-bin killed us. They scored those tries when our man was in the bin and once they went out to 23-8 straight after halftime it was too hard to pull back."
Mount Maunganui 41 (Isaac Te Aute 2, Pera Gibbs 2, Matty Axtens tries; Matt Golding 2 cons, 3 pens, drop goal) Rotoiti 8 (Beau Kiel try; Whakataki Cunningham pen)
Other results:
Development One Final: Te Puke Sports 45 Te Puna 43 (in extra time: 30-all after 80 minutes)
Premier Two semifinals:
Paroa 34 Whakatane Marist 27, Arataki 37 Ngongotaha 8
Division One semifinals:
Te Teko 15 Kahukura 10, Ruatoki 25 Papamoa 24
Development Two semifinals:
Opotiki 19 Ngongotaha 12, Waikite 61 Paroa 0
Next week's finals draw:
Premier Two:
Paroa v Arataki at Lawson Park
Division One:
Te Teko v Ruatoki at Dunderdale Park
Development Two:
Opotiki v Waikite at Princess Street Reserve