They trailed by three goals at the break but their key players came to the fore when they needed to.
International defender Casey Williams made life tough for Pulse shooters Caitlin Thwaites and Paula Griffin, while centre Laura Langman was again a ball of energy in the mid-court.
The game was vital for both sides who wanted to keep their hopes of making the playoffs alive and they came into the contest on 10 competition points each.
Any outside chances the Pulse had of making the top-four went up in smoke following the loss and they can look forward to the bye next week, while the Magic will aim to keep their season alive when they head to Auckland for a showdown with the Northern Mystics.
The Magic's ability to remain composed under pressure will serve them well in the coming weeks as a few crunch matches loom if they want to keep their streak alive of making the playoffs every season that the transtasman league has been in existence.
Langman said the team weren't getting ahead of themselves despite moving to fifth spot with the win, which leaves them one victory outside of the top four.
"We've still got a tremendous amount of pressure on us and it's just one week at a time,'' she said in a court-side interview after the game.
Veteran shooter Irene van Dyk will turn 40 later this month but continued to show no signs of letting up as she shot 34 from 35 and was tough to contain in the attacking end.
The Pulse meanwhile struggled with their consistency under the hoop as Thwaites and Griffin combined to shoot 42 from 55, which wasn't good enough to keep the visitors in touch.
Australian import Thwaites has been in fine touch for the yellow-clad Pulse this year but she would have been disappointed to miss seven shots as she finished with 27 from 34 as Williams and defensive partner Leana de Bruin kept her under pressure.
Ten goals wasn't a fair representation of the difference between the teams but the Magic finished a lot stronger and blew the game out in the fourth quarter.
In today's earlier games, the Adelaide Thunderbirds knocked over the Queensland Firebirds 54-49 in South Australia, while the NSW Swifts moved in to fourth spot with a 51-49 victory over the West Coast Fever in Perth.
The Northern Mystics can take an outright lead at the top of the ladder if they defeat the Southern Steel in Auckland tomorrow night.
Waikato/BOP Magic 52 (Irene van Dyk 34/35, Julianna Naoupu 18/23) Central Pulse 42 (Caitlin Thwaites 27/34, Paula Griffin 15/21) 1Q: 12-11, HT: 21-24, 3Q: 38-33