Striker Tommy Semmy continued to prove his worth at international level with two first half strikes giving his side the advantage going into the break.
The first was a delightful finish from a set-piece taken by Lae City Dwellers captain Raymond Gunemba.
Semmy had his second minutes later when his first attempt, a header, slipped from the opposing keeper’s grasp and allowed the 21-year-old to toe-poke home.
The second half was a closer affair for the two sides but neither side could find the back of the net giving the hosts the 2-0 victory.
Malaysia coach Ong Kim Swees said the match was a test for some of the newer members of his squad.
“This is a good match for both teams to benefit from and I congratulate PNG for the win,” he said.
For PNG coach Flemming Serritslev it was vital international experience for his team as they build up to Stage 3 of the 2018 FIFA World Cup Russia™ Qualifiers.
Malaysia will now travel to New Caledonia where they will take on Les Cagous on Wednesday 22 June, before flying to Fiji for their third and final Oceania friendly on 26 June.