The win means New Zealand remain the only unbeaten team after beating defending champions Australia in pool play and world No.4 Jamaica on Tuesday.
Malawi's effort was built around an outstanding defensive effort led by goal defence Caroline Mtukule and keeper Towera Vinkhumbo.
But it was the shooting of Mwai Kumwenda, who sunk 38 from 42, which almost pulled off the upset of the tournament.
The Kiwis stormed out to an immediate six-goal lead, swinging the ball at pace into the circle and forcing Malawi to call a time out after barely two minutes.
They regrouped well after the break, scoring the next three goals as New Zealand's drive in the front third faltered.
The Kumwenda sisters, goal shooter Mwai and wing attack Bridget, built a solid understanding with centre Takondwa Lwazi and the goals started flowing.
The Ferns still went into the first break with a lead, but at 16-13, it wasn't the margin that had been threatening early on.
New Zealand's zone defence picked up a notch in the second stanza, wing defence Kayla Cullen proving a real menace in pressuring turnover ball.
They edged out to a 20-15 lead, but couldn't shake off Malawi in an increasingly physical match.
Shooter Bailey Mes was in mesmerising form, sinking 10 from 11 for the quarter and working the circle well with stand-in goal attack Jodi Brown.
Shannon Francois, running at wing attack, combined well with centre Laura Langman as the Kiwis scored six of the last eight goals in the quarter for a 30-24 halftime lead.
There were still misunderstandings and turnovers, particularly with the circle feed, and Kumwenda's devastating accuracy meant the Queens took the quarter 15-12 and cut New Zealand's lead to 42-39 with 15 minutes remaining.
Maria Tutaia was subbed on for Brown at the last break, and her coolness under pressure - and the occasional deadly long bomb - secured the win for New Zealand.
The Silver Ferns have a rest day on Thursday before finishing their qualification round matches against Uganda the following day.
A win there will confirm top seeding in pool E, and a semi-final clash against the second-ranked pool F team - almost certainly England - on Saturday.
