Goalkeeper Kevin Hartman made three saves for his ninth shutout of the season and the 62nd of his career, tying a Major League Soccer record for most career shutouts.
The Galaxy (10-14-6) are now within 3 points of a playoff spot with two games left after breaking a four-game winless streak. Chivas USA (10-8-12) fell into third place in the Western Conference.
Vagenas scored in the 29th minute with a 10-yard shot off goalkeeper Brad Guzan's right hand. Donovan scored in the 67th minute. And Gordon clocked a goal in the 80th minute with a shot from 13 yards.
Chivas USA played without three of its top five scorers -- Ante Razov, Juan Pablo Garcia and Francisco Palencia -- who were out with injuries.