Dario Zuparic scored the second-half winner for Portland to claim a 2-1 victory.
The victory means Portland have secured a place in next season's CONCACAF Champions League.
The 41-game tournament, which included group stage and knockout rounds, was created to keep the season alive after the breakout of COVID-19.
Major League Soccer's regular season started back on Wednesday with FC Dallas beating Nashville.
MLS have announced they will try and conclude the play-offs in home markets after leaving the tournament bubble in Florida.