The 18-year-old Gambian forward stole the show as Seattle was put to the sword in its own home ground.
The Whitecaps started the scoring in the 12th minute. Jhon Kennedy Hurtado's headed clearance was poor and Daigo Kobayashi sent it right back the other way. Manneh beat Hurtado to the ball in a foot race and finished smoothly under Michael Gspurning to make it 1-0.
Manneh scored his second shortly before halftime. Camilo latched onto a long ball from Young-Pyo Lee and moved past Djimi Traore. When Hurtado moved out of position to cover the Brazilian, DeAndre Yedlin failed to move inside, leaving Manneh to run onto a clever touch from Camilo and finish his 1-on-1 chance.
Manneh, who erased Stern John from the record book as the previous youngest player to score three in a game, wrapped up his hat trick in the 54th minute, again combining with Kobayashi. The pair played a give-and-go to pull the defense out of position before the midfielder put a short pass right onto Manneh's feet, allowing him to silence the typically raucous Sounders faithful.
Mauro Rosales scored Seattle's only goal in the 69th minute. Yedlin's cross from wide right created chaos in the box, and while Osvaldo Alonso's shot was blocked, Rosales would not be denied from inside the area.
Nigel Reo-Coker grabbed his team's fourth goal in the 83rd minute and ended all hope of a Seattle comeback, catching Seattle on the counterattack and finishing between Gspurning's legs after a lengthy run down the right channel.
Vancouver (12-11-9) is now three points out of the playoff spots, although fifth-place LA has a game in hand. The Whitecaps are four points behind fourth-place Colorado and finish the season with consecutive games against the Rapids.
Second-place Seattle (15-10-6) missed an opportunity to take the lead in the Supporters' Shield race and wrap up the Cascadia Cup and must beat rival Portland on Sunday in order to achieve regional bragging rights.