Andrew Wenger made the Union's intentions clear early on in the contest when he shot from distance, before being denied by a smart stop down at the bottom-right corner of the Portland goal.
Philadelphia continued to threaten and they almost found an opener through Sebastien Le Toux, but he was denied when his long-range effort smashed onto the crossbar.
Next up was Timbers man Gaston Fernández, but he saw an adroit bullet from range kept out cleverly down at the bottom corner as the game headed towards a tense finish.
The Union's Wenger put an end to any jangling nerves in the home crowd when he got the team's vital opener, having made no mistake after finding himself in acres of space inside the box.
Philadelphia wrapped the game up with 20 minutes left to play thanks to a cool finish from Nogueira, who was able to bag his fourth goal of the campaign.
The Union made it 3-0 before the final whistle when Nogueira returned to earn himself a brace and secure his side an important home win.