The Timbers (8-2-10) improved to 2-1-8 on the road and moved within three points of Real Salt Lake for first place in the Western Conference.
Portland also pushed its all-time mark to 2-0-2 against the Union.
The game was delayed 40 minutes to open the second half because of severe thunder and lightning in the surrounding area.
Following the delay, neither team was able to muster many scoring opportunities. The Union (8-6-7) had two corner kicks in three minutes of stoppage time but couldn't take advantage.
The Union played without manager John Hackworth, who was ejected from a victory over Chivas USA. Technical Director Rob Vartughian coached the Union.