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In his first game back after a month out with an ankle injury, Johnson returned to his running best to score his 62nd career try early in the second half before helping create a hat-trick for right wing David Fusitu'a.
The Kiwi test No 7 also kicked five goals as the Warriors claimed their first win over the Sea Eagles since 2013 in front of 17,357 fans at AMI Stadium.
Manly shot out to an early 8-0 lead with a try to hooker Apisai Koroisau and two goals to five-eighth Trent Hodkinson, but the Warriors then scored 34 unanswered points with tries to second-rowers Isaiah Papali'i and Tohu Harris giving them a four-point halftime lead.
Johnson's four-pointer and Fusitu'a's hat-trick – which puts him top of the NRL try scorers list with 15 so far this season - sealed the result early in the last quarter, before Manly centre Brian Kelly barged over for his side's second with nine minutes remaining.
Coming off last week's bye round the Warriors lacked timing early on with Johnson kicking the ball out on the full in the first minute. Back-to-back penalties compounded matters before Koroisau ducked over from dummy-half to open the scoring for the Sea Eagles in the fourth minute.
The Warriors missed two scoring chances with a forward pass denying Fusitu'a and centre Gerard Beale going over the sideline, with nine penalties in the opening quarter shifting momentum between both sides.
They found their rhythm in the second quarter with former Manly five-eighth Blake Green – filling in as Warriors captain with Roger Tuivasa-Sheck out injured - delivering short passes for Papali'i and Harris to stroll over for near identical tries on either side of the ruck to make it 12-8 after half an hour.
Johnson took control after the break, backing up Fusitu'a to score under the bar, then picking the Tongan international up on an angled run for his first four-pointer, while the last two tries came from slick backline move and a deft grubber.
The result keeps the Warriors in fourth spot on the ladder and provides them with the ideal start to the second half of the season ahead of a difficult run with next week's away match against the Cowboys in Townsville, before the Kiwis mid-season test against England in Denver on June 23.
Warriors 34 (David Fusitu'a 3, Isaiah Papali'i, Tohu Harris, Shaun Johnson tries; Johnson 5 cons)
Sea Eagles 14 (Apisai Koroisau, Brian Kelly tries; Trent Hodkinson 2 cons, 1 pen)