Seattle had already wrapped up a spot in the quarterfinals.
Michel Brown scored late in the first half for Marathon, and David Estrada added a second-half goal for Seattle.
The Sounders joined Mexican teams Monterrey and Santos Laguna with 4-0-0 records. They will be the No. 3 seed for the quarterfinal round next March. Seattle's opponent won't be set until the conclusion of group play Thursday.
Marathon was second in the three-team group at 1-2-1, and Trinidad and Tobago's Caledonia AIA was last at 0-3-1.
Marcus Hahnemann returned to action in the game. The two-time U.S. World Cup and 13-year English Premier League goalkeeper signed with the Sounders on Sept. 14.