Manneh, 18, was the fourth player selected in the MLS draft this year and had scored twice in 17 games for the Whitecaps.
He produced a breakout game on Wednesday, scoring in the 12th, 42nd and 54th minutes to give Vancouver a 3-0 lead.
Vancouver (11-11-9) had just one win in its previous eight games. The Whitecaps moved into seventh place in the Western Conference, six points behind fifth-place Colorado. The top five teams in each conference earn a playoff bid.
Seattle (15-9-6) missed out on a chance to jump past Real Salt Lake into first place in the West.
Vancouver also came up with a goal from Nigel Reo-Coker, his first in MLS.