Playing for the first time since tearing a groin two months ago, Munster came off the bench for the Storm but still played 52 minutes at five-eighth.
The Queenslander finished Friday night at CommBank Stadium with a solid hit out, but Melbourne will mostly just be relieved to have their main man back.
Melbourne were well below their best, while the Eels spent large periods of the game camped on the visitors' tryline after leading 8-6 early.
The Storm did not play the ball inside the attacking 20-metre zone until the 47th minute, and had two plays in total there for the match.
In contrast, the Eels spent large portions of the match camped on Melbourne's line, and had 41 plays in the attacking red-zone.
But there is a reason why the Storm are now six points clear at the top of the ladder after seven straight wins, and Parramatta are battling to fight off the wooden spoon.
Cameron Munster played a solid 52 minutes for Melbourne on his long-awaited return. (Mark Evans/AAP PHOTOS)
The Storm's first two tries were both direct results of Eels errors, and another came largely as a result of a Will Warbrick linebreak from within his own end.
"I saw that stat (about red-zone tackles)," Storm coach Craig Bellamy said.
"If someone told you that before a game you would think the other side would've won.
"We were just really untidy coming out of our own end ... But on the bright side we defended that well."
Still, there were reminders of why Melbourne loom as the biggest threat to Penrith's bid for a four-peat.
Playing their first-choice spine for only the sixth time this year, fullback Ryan Papenhuyzen broke down field in the lead up to the first try and scored another himself.
Halfback Jahrome Hughes worked over Parramatta's edges, and threw a smart pass back to Warbrick for his four-pointer.
Even hooker Harry Grant scored a try, when Eel Shaun Lane spilled a ball straight into his hands and he went 40 metres untouched.
And then there was the crucial fitness of No.6 Munster.
"We didn't expect him to go setting up tries or running 100 metres to score tries," Bellamy said.
"Obviously his match fitness is not great. We just wanted to ease him back in and get his timing right."
Ryan Papenhuyzen was among five try-scorers in a comprehensive display from the Storm. (Mark Evans/AAP PHOTOS)
The Storm also appear to have more strike than in recent years, with Eliesa Katoa again good on the right edge.
But an apparent leg injury to his back-row partner Shawn Blore was the only concern for the Storm, after he left the field in the second half.
Parramatta remain two points ahead of Wests Tigers at the bottom of the ladder, with the same number of wins.
With next year's coach Jason Ryles in full planning mode, there were glimpses of promise early in the way the Eels were able to take a lead.
Dylan Brown put a lofted cut-out ball on a dime for Sean Russell to score one try, while a Shaun Lane offload helped Jake Tago cross.
But for those passages it would have been tough viewing for Ryles, as the Eels slumped to a sixth straight loss with 10 of their regular starting players out injured.
"Class probably prevailed in the end," interim Eels coach Trent Barrett said.
"If you had (Mitch) Moses, (Junior) Paulo and (J'maine) Hopgood it might be a different story. You'd like to get a crack at them full strength."
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