After a slow start to the game, Megan Bell squandered a good chance to open the scoring on the half-hour mark.
The Linfield midfielder burst into the box to latch onto Holloway’s raking pass but saw her tame effort drift wide.
The away side then broke the deadlock on 40 minutes as Mason rose highest to meet an inviting corner from Bell and power home a header for her first international goal.
That goal sparked Malta into life as they extinguished NI’s lead less than a minute later, hitting back through Farrugia, who volleyed into the roof of the net.
Malta almost went ahead just before the break when Jackie Burns was called into action to thwart Haley Bugeja after Farrugia had unselfishly squared to her teammate.
NI made a bright start to the second half and were rewarded with a second goal on 51 minutes as Mason pounced on a loose clearance from Malta to fire a low first-time shot into the bottom corner from outside the box.
They extended their advantage on 69 minutes when Johnson turned home from substitute Danielle Maxwell’s corner for her first NI goal.
McArdle’s side then had Holloway sent off for as she received a second yellow card a foul on Kailey Willis, but they responded well to going down to 10 by adding a fourth goal on 72 minutes.
McFarland raced onto a long ball forward, held off Oceane Grange and arrowed a shot into the far corner for her first international goal.
Substitutes Ayres pulled a goal back for Malta eight minutes later, capitalising on a defensive lapse from Rebecca McKenna to blast past Burns, but NI saw out the victory which moves them a point behind Turkey in second before the two teams meet in June.