Ekpo scored from 10 yards into the lower-left corner for his first goal since May 9, 2009.
Chivas (3-4-4) led 2-1 at halftime on goals by Nick LaBrocca in the fourth minute and Andrew Boyens in the 37th. Mendoza scored in the 17th off a pass from Ekpo — his first assist since May 26, 2009.
Mendoza tied it for the Crew (3-3-5) in the 52nd, and Jorge Flores gave Chivas the lead 5 minutes later.
Flores was ejected for a second caution in the 69th minute.