Playing at the back for a second week, Munster again starred to help the Storm make their case for an eighth straight season in the NRL's top four.
It came as Penrith's title defence took another hit, with Liam Martin suffering suspected ankle syndesmosis while Moses Leota was later cleared of injury with cramp.
The Panthers are far from panicking, given they sit well clear at the top and were without the injured Jarome Luai, a banged-up Dylan Edwards and suspended pair Nathan Cleary and James Fisher-Harris
But the Storm are a team clearly back in their groove after losing four straight games last month.
Missing Ryan Papenhuyzen, Jahrome Hughes and Felise Kaufusi themselves, they withstood more than 40 play-the-balls in their own 20-metre zone.
Time and time again they turned the Panthers away, becoming the first team to hold Penrith scoreless since way back in June 2015.
The win moved them two points clear of fifth-placed Parramatta and well above them on for-and-against, with the chasing pack one win further back.
Melbourne have to play Brisbane, the Sydney Roosters and Eels on the run home, but now look as if they are ready to match it with any of the trio.
Regular playmaker Munster was again crucial, with Craig Bellamy now considering using him more at fullback with Ryan Papenhuyzen out for the year.
A week after scoring a hat-trick on his return to the No.1 jersey after almost five years, Munster was just as influential in defence as he was in attack against the Panthers.
With Penrith dominating the ball in the second half, he pulled off a crucial try-saver on Brian To'o early on to keep Melbourne's lead at 16-0.
From the next set he was able to swing the momentum in the Storm's favour, breaking downfield to put them on the attack.
"He really enjoys playing fullback because it gives him a bit of freedom," Bellamy said.
"I'm not quite sure that we will stick to Munster at fullback all the time.
"We will probably look at it on our opposition, and what we think the best way to use Munster and (Nick Meaney)'s strengths."
The 27-year-old also had a role to play in the Storm's first try.
Given the freedom to roam at the back, Munster went shortside after a scoreless opening 18 minutes and helped put Justin Olam onto the attack before the centre kicked back for Meaney to score.
Brandon Smith went over from the next set, busting through Martin and Leota from the halfway line to make it 12-0.
Late season recruit David Nofoaluma got Melbourne's third try after a nice Jesse Bromwich offload just before the break, before the Storm held on through a scoreless second half.
"They were very desperate tonight, probably more than we were," Panthers coach Ivan Cleary said.
"I felt like there were some combination issues tonight (with the guys out), and when you play a good team and a good defensive unit, it shows up there."
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