Houston prevailed over D.C. 4-2 on aggregate after a 1-1 draw in Washington, while the Galaxy also advanced on a 4-2 score despite losing to Seattle later in the day 2-1.
The results set up a rematch of last year's MLS Cup title game in Los Angeles on December 1.
Already having secured berths in this season's Champions League quarterfinals in March, Houston and Los Angeles join U.S. Open Cup champion Sporting Kansas City and the MLS Supporters' Shield winner San Jose Earthquakes for next year's confederation championship with the United States' four berths.
It will be the Dynamo's second straight and fourth overall appearance in the Champions League, while the Galaxy qualified for the fourth straight year.
The Galaxy is set to play Herediano in the quarterfinals in March, while the Dynamo will face Santos Laguna.
Both Los Angeles and Houston have reached the quarterfinals in two of their three appearances in the Champions League.
The results also will see Seattle's three-year run in the Champions League end. It has qualified for the current season's quarterfinals and will play Tigres, D.C. United played in the first two seasons of Champions League, but has not qualified since.