Portland sent the No. 17 selection and defender Andrew Jean-Baptiste to Chivas USA on Thursday for the No. 2 pick and midfielder/defender Jorge Villafana.
Zakuani has played for the rival Seattle Sounders since he was the top pick in the 2009 MLS SuperDraft. He has appeared in 80 regular-season matches, with 17 goals and 14 assists.
Zakuani played for Timbers coach Caleb Porter at the University of Akron and led the nation in scoring with 20 goals and 47 points as a sophomore.