Longo volleyed in the game's final goal two minutes into second half stoppage time.
Football Ferns coach Tony Readings said Papua New Guinea's tactics proved a tough nut to crack in stifling conditions.
"It was a lot hotter than it was in the last game," Readings said, "and Papua New Guinea employed completely different tactics to Tonga which they executed brilliantly.
"Against Tonga we were able to get in behind the defense but often with Papua New Guinea they put all their players behind the ball and it meant that it was difficult in the conditions to be able to break down a very compact defense.
"But we still created a whole bunch of chances so that's another thing we need to keep working on because we should have put the game to bed a lot earlier than we did."
After a 1-1 draw in Monday's match between the Cook Islands and Tonga, the Football Ferns can secure their passage to Canada on Wednesday with a draw against the Cook Islands and Readings says the focus in game three will be about applying the knowledge gained from both outings so far.
"There are a lot of learnings we can take from both games and we want to leave this tournament on the most positive note we can so it sets us up well for the big games we've got coming up next month."
Wednesday's match against the Cook Islands kicks off at 2pm (NZ time).
Oceania Nations Cup 2014
Papua New Guinea 0-3 Football Ferns (half: 0-0)
NZF: Rebekah Stott 59', Amber Hearn 70', Annalie Longo 90+2'
PNG: -