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 the opening 40 minutes 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.
The Eagles were first on the scoreboard 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, who scored four tries last round, somehow 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 perfectly-weighted 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 Xavier Coates collecting the spoils.
Winger Coates, also backing up from Queensland's Origin triumph, then iced the win in the 73rd minute with a spectacular dive in the corner to secure his double.
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