With State of Origin star Munster donning a mask to watch from the coaches' box after being ruled out due to a virus, the Storm shrugged off an ugly first half to roar home at AAMI Park.
Melbourne led 10-6 at halftime but had no right to be in front with the Sea Eagles dominating early and Munster's Maroons halves partner Daly Cherry-Evans in vintage form.
The Storm's attack faltered with eight errors for a 68 per cent completion rate yet they still managed to bag two tries before adding another three unanswered before fulltime, with winger Xavier Coates scoring a double.
"The first half wasn't great - we didn't complete that well although we did a pretty good job defensively to stay in it," Storm coach Craig Bellamy said.
"We had to work a lot harder than what we should have.
"We really put a stamp on it in the first 10 or 15 minutes of the second half and that's basically where we won the game."
Manly coach Anthony Seibold felt his team couldn't capitalise on their early gains, but lauded the efforts of Reuben Garrick, who replaced the injured fullback Tom Trbojevic.
"We were really good first half, defensively we were really strong, but in the second half our lack of accuracy and detail, in attack in particular, just put too much pressure on defence.
"Our attack just wasn't good enough."
The Sea Eagles opened the scoring in the 13th minute with second-rower Haumole Olakau'atu splitting the Storm defence to ground a grubber by Cherry-Evans.
Melbourne hit back when winger Will Warbrick managed to fling the ball back into play as he was going into touch, with Jahrome Hughes scooping it up and diving over the line.
Trailing 4-6, the home side hit the front with three minutes left in the half when Hughes put a kick into the in-goal and Munster's replacement Jonah Pezet got a hand to it.
Manly hooker Lachlan Croker was forced off early in the second half after a hit by Storm forward Aaron Pene, who was put on report for the tackle.
Pene left the field himself a minute later, limping off with an ankle injury after getting tangled in a tackle, while Croker passed his HIA to return.
With Pezet finding his rhythm, Melbourne reined in the errors in the second half and reaped the rewards, taking advantage of two Manly mistakes to score.
Prop Sean Keppie knocked on at the first tackle with Pezet and Hughes combining before Nelson Asofa-Solomona, who started in the second row, proved unstoppable.
The home side pushed the lead out to 14 points when a Pezet kick was tipped ahead by scrambling Manly winger Ray Vaega, with Coates collecting the spoils.
Also backing up from Queensland's Origin triumph, Coates iced the win in the 73rd minute with a spectacular dive in the corner to secure his double.
Bellamy said Coates' effort was amazing coming off Origin, finishing with 190-run metres.
"Xavier was our best player," he said.
"He was outstanding in that first half and I didn't think he was going to be able to repeat it in the second but he did, three days after an Origin game, so he was tremendous."
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