Zapata put the home side 1-0 up after 16 minutes when he slid in and finished off a delicious low cross from Juan Cuadrado.
His Atalanta teammate Muriel made it two nine minutes later when he scored with a first-time shot from 10 meters out.
Muriel then got Colombia's third just seconds before the whistle, when he completed a rapid counterattack.
Colombia took their foot off the pedal in the second half but Venezuela could make no impact and neither side added to the scoreline in a calmer second 45 minutes.
The top four teams in the 10-team South American group qualify automatically for the finals in Qatar in 2022 and the fifth-placed side will go into an inter-regional playoff.