Seed germination and the establishment of young seedlings are critical phases in the plant’s life cycle. To control these processes, plants have evolved diverse hormonal signaling networks in which brassinosteroids (BRs) attenuate abscisic acid (ABA) responses; however, the underlying regulatory mechanism remains elusive. Here, we reveal that epigenetic silencing of the ABA signaling regulator ABI3 via the BR-related transcription factor BES1 is essential for the inhibitory effect of BRs on ABA signaling during early seedling development. BR-activated BES1 forms a transcriptional repressor complex with TPL via its EAR motif that recruits the histone deacetylase HDA19. This facilitates the histone H3-mediated deacetylation of ABI3 chromatin, leading to the suppression of ABI3 and its downstream target ABI5, which results in reduced ABA sensitivity. We propose that the BR-activated BES1-TPL-HDA19 repressor complex controls epigenetic silencing of ABI3 and thereby suppresses the ABA response during early seedling development.