The Galaxy won the two-game series with a 3-1 aggregate total, including their 1-0 win in Harrison, N.J., on Sunday, and will be appearing in their third consecutive conference championship. The Supporters' Shield winners next face Real Salt Lake with a spot in the MLS Cup on the line.
Luke Rodgers put the Red Bulls ahead less than 4 minutes in, tying the aggregate at 1-1.
Mike Magee scored for the Galaxy in the 42nd minute on a header of David Beckham's corner kick.
The Galaxy were awarded a penalty kick when New York defender Roy Miller shoved Beckham down from behind in the box.