Ngongotaha's Harlem Simiona wrapped up the three points when he claimed a late goal.
Senior player Josh O'Sullivan said it was a great win for the club.
"It was a ripper. It was the game of the season for us," he said. "Everyone in the team played well you couldn't really pick a player of the day."
He said they went into the match knowing they had to win to keep their title hopes alive.
Ngongotaha still have 10 games left to play. O'Sullivan said they would simply take it a game at a time.
"We are still trying to take it game by game and not looking too far ahead," he said. "Now we have knocked off the top team everyone will be targeting us, so we have to push on."
Meanwhile, Rotorua United were beaten 1-0 by Melville United on Saturday at Neil Hunt Park.
- Premiership table: Cambridge 34, Ngongotaha 29, Melville 27, Papamoa 21, Tauranga Old Blues 19, Waikato Unicol 17, Rotorua United 16, Matamata 16, Katikati 16, Otumoetai 13, Tauranga City 9, Tauranga Boys' College 5.