With the visitors sitting two places and one point behind Ngongotaha before the game, manager Stephen Towers said a win was crucial.
"That's 11 goals in two home games, back-to-back victories - that gives me confidence. This was a six-pointer for us and I thought the gap - in terms of football - well there's a bit of a gulf between us and them.
This is Ngongotaha's first season in the Northern League second division, with the aim to secure their position in the league this season.
"I can't see [Onehunga Mangere] picking up many more points, but I can see us picking up a lot now.
"We were pretty dominant, but to their credit they gave it a go. Their two goals were against the run of play really, they didn't really hurt us, but we let in two goals which is disappointing."
Waller, playing at centre half, was named man of the match for the home side.
Next Saturday Ngongotaha travel to Auckland to take on Te Atatu, who lost to table-toppers Fencibles Utd 3-1 on Saturday. Te Atatu are two points and one place below Ngongotaha in ninth in the 12-team division.
Ngongotaha should be able to welcome back Luke Barker who missed Saturday's game with an ankle injury.
■ In the WaiBOP Premiership, Rotorua Utd drew 1-all with Melville in Hamilton.