A fifth loss in seven games came away to the MSL's table-proppers who had only won twice at home all season
The match, played out infront of a near-empty Shah Alam Stadium, was decided just seconds after the start of the second period of play with Patrick Wleh grabbing the match winner.
It took just under half-hour of play for the opening goal to be scored. LionsXII who had dominated proceedings from the start took the lead through a fine individual effort from Gabriel Quak who ended his long-running scoring duck.
Quak was given plenty of time and space by the PKNS defence who backed off from his run, and the Singapore international fired in a shot from outside of the penalty box to beat Remeze Che in goal.
But the lead lasted all of five minutes, when Arip Amiruddin latched on to a fine through ball and outran Faritz Hameed to slot the ball through the legs of the onrushing Izwan Mahbud to get the game back on level.
Just moments earlier Wleh had been denied a strong penalty claim after being brought down by Izwan in the penalty box.
The Singapore side were also left ruing another decision when PKNS custodian Remeze Che Omar kicked out at Afiq Yunos but was lucky to be let off with just a yellow card.
Fifteen seconds after the restart, however, Wleh timed his run perfectly to get on the end of Faiz Isa's long ball and left Baihakki Khaizan trailing as he made his way into the penalty box and rifled in a shot past Izwan from close range.
A surprise lead for the struggling home side was soon met with time wasting antics as players hit the ground to run the clock down.
Wleh proved to be a constant threat for the LionsXII defence but was also guilty of passing on his chances. LionsXII meanwhile were also lucky to see Faris Ramli stay on the pitch after the winger looked to have gone in hard on Remeze and was given only a yellow card.
LionsXII struggled to break the stubborn PKNS defence down and were themselves unable to create noteworthy chances in the final third.
Safuwan Baharuddin playing in a more offensive role had claims for a handball turned down, and with three minutes to go, Sufian Anuar scuffed a clear chance from inside the six-yard box.
The defeat leaves Fandi Ahmad's side on 25 points with two games left to be played. It also marked the fifth loss in seven games for the defending Malaysian Super League champions.