The home side took the lead in the ninth minute when they were awarded a free kick on the left. Brad Davis whipped a dangerous cross into the box and Bruin rose to power a header into the bottom corner.
Bruin almost doubled his side's lead when he controlled a goal kick from Tyler Deric and fired a 20-yard volley at goal which went just over the crossbar.
In the second half, the Timbers managed to pull level as they took advantage of a collision in midfield. Diego Valeri put a low ball into the penalty area for Fanendo Adi to fire past Deric from close range.
Bruin nearly restored the Dynamo's lead when he collected a pass from Davis on the edge of the box, but his right-footed drive went just wide of the post.
However, one minute later, Giles Barnes did put Houston back in front as Alexander Lopez pulled the Portland defence one way and then the other to set up the midfielder, who blasted a strike into the top corner.
Houston are fourth in the MLS Western Conference, while the Timbers sit five places below them in ninth.