In a high-scoring affair, the Sea Eagles overcame a 30-18 defect to end finish the game ahead.
Manly opened the scoring in the first half with a try to James Mirceski in the 10th minute, which was easily converted by Regan Haika.
The Eels quickly hit back, with Vai Toutai scoring in the corner off the back of an impressive flick pass from John Folau.
A short time later the Blue and Gold were in front, with Sam Gorman pushing through the Sea Eagles line to score right in front of the posts.
Michael Stig from the Sea Eagles levelled things up with a quick try off a penalty, but a repeat performance from Folau and Toutai saw him score his second in the corner, putting the Eels ahead 18-12 at the half time break.
Manly again scored first in the second half, through a strong attacking set ending up in Matt Ikkuvalu's hands.
But it wasn't for long - Eels bench-man Tui Kamikamica scored a phenomenal try in the corner for the Eels, beating four Manly defenders in the process. Mitchell Brasington was again on the money, with his second sideline conversion sailing between the uprights.
Will Bugden added another try for the Eels before a return try from Latrell Schaumkel.
Patrick Kennedy levelled the scores after taking the high bomb to score a try, with the conversion bringing things level at 30 apiece.
Fabian Goodall added the finishing touch for the Sea Eagles, with the final conversion missed.
The young Eels side put up a spirited attempt to even scores up at, but were eventually unsuccessful.
SEA EAGLES 34 (Mirceski, Stig, Ikuvalu, Schaumkel, Kennedy, Goodall tries, Haika 5 goals)
EELS 30 (Toutai 2, Gorman, Kamikamica, Bugden tries, Brasington 5 goals)