Hayne's opposite number Brett Stewart levelled the scores when the Sea Eagles exposed the Eels down the left but hooker Matt Keating dived over from short range to retake the lead midway through the first spell. Hayne then produced a magnificent cut-out pass to put Ken Sio over in the corner.
Manly scored either side of halftime to take the lead before Eels five-eighth Ben Roberts found an unmarked Hayne to score between the posts in the 61st minute.
Two late penalties and a field goal from halfback Chris Sandow ensured the Eels would get their first win of the season, though they remain bottom of the table.
Kiwis centre Steve Matai made his return from injury and had a terrific match, making plenty of metres with the ball and produced a couple of his trademark huge hits to remind the national selectors what a good player he could be in the upcoming test against the Kangaroos at Eden Park.
Eels prop Fuifui Moimoi was back to his damaging best in this game - another sending a reminder to Kiwis selectors.
The Sea Eagles had skipper Jamie Lyon ruled out with injury before kickoff, joining rep stars Glenn Stewart and Tony Williams on the sidelines.
In a concern for both the Sea Eagles and the New Zealand test selectors, five-eighth and test certainty Kieran Foran limped from the field late in the game with a hamstring injury.
Eels lock Reni Maitua faces a spell on the sidelines after being placed on report for a nasty high tackle on Stewart.
After starting their title defence with two strong performances, three straight losses see Manly remain well outside the top eight at the end of the round and new coach Geoff Toovey searching for answers.
Eels 29 (J. Hayne 2, M. Keating, K. Sio tries, C. Sandow 6 goals, Sandow field goal), Sea Eagles 20 (B. Stewart, A. Watmough, J Taufua, J. Buhrer tries, D. Cherry-Evans 2 goals). Halftime: Eels 18-10.
