Ngatapa increased their lead to 13 by halftime, with attackers Natalie Knight and Lara Gillies netting 15 times between them.
Whangara were 10 goals adrift at the end of the third quarter before attackers Vianney Douglas and Nadia Taare pulled back the deficit. Whangara equalised with less than two minutes left.
Whangara scored the winning goal in the dying seconds of the game to book a semifinal against High School Old Girls on Wednesday.
Whangara coach Ronnie Martin said her team had only seven players to choose from but she praised their performance in getting back into the game.
She was particularly pleased that they were able to outscore Ngatapa 19-8 in the final quarter.
“We were down by 13 goals halfway through that game. Going into that final quarter we were 10 down, but then Ngatapa called a break for injury. We were just four down then, so I had to just motivate them to keep going.
“We have a team of players who know how to play finals netball and are quite experienced at it. We only have seven players but we’re going to motor on.”
Meanwhile, Horouta Gold’s 37-42 loss to Gisborne Girls’ High School Hydraulink in the bottom four playoffs means the Golden Girls end the season in eighth place.
In the remaining bottom-four game, last year’s champions Nga Hau e Wha beat Claydens Waikohu 57-47.