Shortly after halftime, Ngongotaha made it 2-0 when Harlem Simiona bet a player and rifled a shot past the keeper.
Simiona had an impressive game yesterday and entertained the crowd during a great battle with South Auckland captain, and right back, Sailesh Singh.
As the game entered the final 20 minutes it looked like Ngongotaha would comfortably take the chocolates.
But an error from goalkeeper James Towers saw South Auckland snatch a goal back.
The intensity picked up as South Auckland went in search of an equaliser. However, O'Sullivan scored his second with about 10 minutes left to make it 3-1.
South Auckland grabbed one more goal late in the match to make it 3-2 but substitute Jordan McKay closed out the game for Ngongotaha with a goal of his own in the dying minutes.
Ngongotaha will now go into a random draw with the remaining sides from the Northern Region, which includes most of the top teams from Auckland.
O'Sullivan said it was a massive result for the club to make it to the top 32 and they would be happy to draw any of the top teams. "Give us the hardest, send us your best," he said about the draw.
He said they played well and they dedicated the win to their coach Shane Davis.
O'Sullivan said when South Auckland pulled a goal back to make it 2-1, he recalled their tough defeat two days earlier against Cambridge. Ngongotaha conceded two late goals to lose that Waibop Federation One match on Saturday.
"I honestly thought about Saturday when [Cambridge] got two goals in three minutes, and I was thinking not this again."
O'Sullivan said he was hugely proud of his teammates for winning the match yesterday.
The long-standing Chatham Cup competition has been running for 91 years and is the most prestigious club trophy in New Zealand football.