The Warriors looked to have the match in the bag through 60 minutes of play, before the under-manned Panthers exposed shaky tackling to score with three minutes left, then former Warriors pivot Maloney delivered a field goal killer blow.
Even a stunning second half try by a flying David Fusitu'a - a contender for try of the season - couldn't get the home side the win.
Warriors centre Patrick Herbert kicked a 40 metre penalty goal to send the match into extra time, but that turned the game into the Maloney show, as the Warriors slumped to another loss in Auckland.
Penrith overcame two yellow cards and an 11-5 penalty count, leaving Warriors coach Stephen Kearney with a tough Monday morning review ahead of him.
Rubbing salt into the wound, the Warriors will also likely be without the services of Nate Roache for a while, the young hooker suffering what appeared to be another serious knee injury.
The Panthers did start the match the better of the two sides, and looked good shifting the ball to their edges in the opening exchanges by running big Viliame Kikau at Blake Green to great effect.
But it was the Warriors who got on the board first through Peta Hiku, who crossed to score against his former club first after just eight minutes after some great lead up work from his halves.
It was all the Warriors early, as Green was able to control field position and starve Penrith of possession.
But while there was plenty of intent with the ball, defensively the home side were falling off tackles left and right.
And off the back of some poor discipline, Penrith easily crossed for their first through James Tamou after 20 minutes of playing mostly in their own half.
Maloney converted to give the visitors a 6-4 lead.
The Warriors looked to have answered back through hooker Karl Lawton moments later, only for his dummy-half attempt to be turned down by the bunker for an obstruction.
They would settle for two points of the tee shortly after, the Panthers continuing to infringe inside their own 10m zone.
Things went from bad to worse for Penrith, with Liam Martin sent to the sin bin - the unfortunate casualty of nine first half penalties.
Three minute before halftime Warriors then rubbed salt into that wound through prop Bunty Afoa, who crashed over to score his side's second from 10m out.
Herbert converted from beside the uprights and the Warriors went into the sheds 12-6 up.
Two minutes into the second and the Panthers were down to 11 men, with Jarome Luai was sent to the bin for taking out Warriors skipper Roger Tuivasa-Sheck in a scoring position.
Immediately the Warriors shifted to the edges and a flying Fusitu'a went in to score the Warriors third - and a contender for try of the season in the process.
But the visitors wouldn't go quietly and 15 minutes into the second, centre Brent Naden pounced on a perfectly weighted Maloney kick to score and draw his side to within four points.
An arm-wrestle ensued and Penrith were able to control field position for much of the second half.
Brent Naden then broke out from his own end to score a brilliant solo try and looked to have won the match for his side with just two minutes left on the clock.
The Warriors went short from the kick-off and earned the vital penalty that Herbert was able to nail and send the match to golden point.
But the visitors kicked the vital one pointer to crush the Warriors hearts in the 90th minute.