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 knockout round next March on the basis of their plus-7 goal differential. Monterrey is the top seed at plus-15, and Santos Laguna is No. 2 at plus-12. Seattle's opponent won't be settled until after 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.
Ochoa opened the scoring in the 23rd minute with his team-leading fourth Champions League goal. Mario Martinez settled the ball near the right corner flag, crossed it into the penalty area, and Ochoa ran onto it from 8 yards straight in front, firing into the back left corner.
Zakuani made it 2-0 just before the end of the 27th minute. He took a short pass from Jeff Parke up the left side, went into the box and curled a 16-yard shot around the left post.
Marathon got one back from Brown on a well-executed counterattack late in the 37th minute. Mauricio sent a long ball down the right side where Tulio Vega caught up with it and took it into the box, drawing Sounders goalkeeper Marcus Hahnemann off his line. Vega sent it across the goalmouth, and Brown slammed it into a wide-open net from in front of the left post.
Estrada finished the scoring in the 76th minute.
Hahnemann, a two-time U.S. World Cup team member and 13-year veteran of the English Premier League, made four saves in his first game for his hometown team since signing Sept. 14. It was his first competitive game since Jan. 30, 2011, when he was in the net for Wolverhampton in a 1-0 English FA Cup loss to Stoke City.