First-half goals from Luis Vargas and Edson Mendoza set up the win for Julio Quintero's men, who are 14th in the Apertura.
Leomar Pinto pulled a goal back for Caracas in the second half, but the loss was their second straight in the league and left them fourth.
Caracas are four points adrift of league leaders Trujillanos with four games remaining.
Vargas' 24th-minute penalty sent Zamora on their way and they doubled their lead a minute before the break through Mendoza.
Pinto gave the visitors hope with his goal in the 55th minute, but they were unable to find an equaliser.