Den Haag dominated the early stages and Edouard Duplan had a seventh-minute chance to give the home side the lead before Rick Dekker opened the scoring for Zwolle after 44 minutes, receiving the ball from Lars Veldwijk before shooting into the top corner.
Veldwijk secured the victory when he shot home from an acute angle in second-half stoppage-time.
The three points lifted Zwolle up to seventh in the table and into a Europa League play-off spot while defeat left Den Haag in 11th place, five points behind their opponents.