Nguyen, waived by Vancouver in March, made his former mates pay with his first two career goals.
His first tally came in the 6th minute when the ball deflected off the back of Vancouver's Young-Pyo and erased a 1-0 Vancouver lead.
His second, coming in the 72nd, was scored on a spectacular volley from 25 yards out off a Chris Tierney throw-in, wrapping up the scoring for New England (4-6-0).
Saer Sene and Shalrie Joseph also scored for the winners.
Eric Hassli scored for Whitecaps FC (5-3-2).