This study investigated the effects of Ganoderma boninense infection, the causal pathogen of basal stem rot (BSR) in oil palm, and biological control by Trichoderma asperellum on defense-related enzyme activities and morphological traits of oil palm seedlings under greenhouse conditions. Ganoderma infection increased phenylalanine ammonia-lyase (PAL) activity in oil palm seedlings at the early stage of inoculation. T. asperellum T76-14 induced the activities of PAL in leaves and polyphenol oxidase (PPO) in roots. PPO activity increased significantly in Ganoderma-infected and Trichoderma-treated seedlings compared to that in untreated control. Except for the chlorophyll concentration, no significant differences were observed between the treatments in plant height, foliar length, stem girth, number of fronds, or plant dry weight. No external symptoms of BSR disease appeared within 20 weeks in all treatments. However, necrotic tissue was observed inside the boles and G. boninense K4/2 DNA in the root tissues and soil samples of Ganoderma-infected seedlings but not in Trichoderma-treated seedlings. These findings provide insights into the responses of oil palm seedlings to G. boninense K4/2 and T. asperellum T76-14 and will be useful for developing an alternative method to control BSR disease in oil palm at an early stage.