Northland tied things up just before the break through Finn Diamond to set up an interesting second stanza.
It was a cagey affair in the last 45 minutes however Papakura broke the deadlock once again through Heather nailing the penalty kick.
Northland hadn't lost a game at home this season and weren't going to let Papakura break that streak as captain Steve Schimmel looked to have secured at least a draw with a strike with 10 minutes left.
Papakura had other ideas and Heather clinched the victory deep into injury time.
Northland coach Dan Johnston said they were disappointed but he's happy with how the team has progressed throughout the season.
"We're gutted. I don't feel we were at our best today, but the fact that we took them all the way shows how far we have come this season," he said.
"It's still up to us in terms of our final league position, but we know we are going to have to be at our best if we are going to get anything from Fencibles next week."
Northland head away to Riverhills Park for their final league game next week.