However, the Villagers held on to secure the precious 2-0 victory.
Ngongotaha coach Shane Davis said his team performed well, bouncing back from a disappointing loss to Cambridge last weekend.
"A much improved performance," he said after the game. "It was a real team effort."
The victory sees Ngongotaha close in on the top two sides in the competition, AFC Fury and league-leaders Tauranga Old Blues.
Meanwhile, Rotorua United have added to their disastrous start to the season.
They faced Whakatane Town at Neil Hunt Park, and it took only 90 seconds for Whakatane to take the lead when a cross found their striker in the box and he was unchallenged to head home the opening goal.
Just minutes later it got worse when Whakatane made it 2-0 from a penalty.
The visitors dominated the game from that point on with a speculative 45m shot drifting over keeper Andrew Gibbs to make it 3-0 at half time.
United played with more purpose for the rest of the game but were unable to put one into the Whakatane net.
Matamata bet Melville 3-1, Waikato Unicol bet Otumoetai 2-0 while Tauranga City held competition leaders Old Blues to a 1-1 draw.
Division two results:
Cambridge 0 HRFC 5, Rotorua United 1 West Hamilton 2, Old Blues 1 Tauranga City 1, Papamoa 4 Matamata 1.