Up 14-6 at halftime after scoring three tries, Parramatta could cross only once after the break as the Sea Eagles clicked into gear.
It comes after the Eels conceded eight second-half tries to the Dolphins last week in Darwin, putting the spotlight on coach Brad Arthur.
Parramatta were much improved on Friday night, with Maika Sivo scoring a hat-trick and Ethan Sanders offering some good signs on debut.
But ultimately their discipline and goalkicking cost them, with Clint Gutherson and Dylan Brown landing a combined one goal from five attempts.
Reuben Garrick was key to Manly's comeback with two second-half tries as the Eels capitulated. (Anthony Kourembanas/AAP PHOTOS)
Reduced to 12 men with 22 minutes left, the Eels got back to 20-18 when Maika Sivo crossed in the corner after a kick, with Will Penisini off the field for a professional foul.
But the winger went from hero to villain moments later, sin-binned for putting his forearm into Rueben Garrick's face on the fifth tackle.
Manly capitalised immediately, with Haumole Olakau'atu providing an offload for Garrick to go over two plays later.
And when Garrick crossed again down Sivo's side with the winger off the field moments later, the contest was over.
The win momentarily lifts Manly into the NRL's top four with five wins and two losses - their best start to a season in 10 years.
The victory could still come at a cost, with Olakau'atu facing a possible ban after being sin-binned for a dangerous throw on Shaun Lane early.
At that point the Eels had all the early running, with five-eighth Sanders running the ball confidently and Parramatta producing offloads at will.
Maika Sivo shone with three tries but it was not enough to stop another Eels fade-out. (Grant Trouville/AAP PHOTOS)
Sivo scored twice in the first half alone, both times catching rival winger Jason Saab out when Parramatta ran the ball on the last tackle.
But just like in Darwin last week, halftime stunted Parramatta's momentum.
Manly crossed twice in the space of five minutes after the break to take the lead, with Cherry-Evans putting Saab into space in the lead up to one try before finishing another himself.
It was down his right edge that Manly were at their best, with Olakau'atu, Garrick and Saab busting 15 tackles between them and all second-half tries coming down that side.
And while Parramatta briefly threatened to fight back, they remain 14th on the ladder with a 3-5 record.
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