Inspired by Chinese Buddhist scholar-monks' interest in Dignāga's Investigation of the Percept (Ālamabanaparīkṣa) during the sixteenth and seventeenth centuries, Japanese scholar-monks also composed several commentaries on this epistemological treatise during the Tokugawa era. Unfortunately, these Japanese commentaries are preserved only in manuscript form and have not received the attention of modern scholars. Aiming to complete the historical picture of the reception of Dignāga's Ālamabanaparīkṣa in early modern East Asian Buddhism, this paper focuses on Kiben's 基辨 (1718-1791) and Kaidō's 快道 (1751-1810) commentaries to examine their analysis of Dignāga's syllogism. According Kuiji 窺基 (632-682), Dignāga composed the first three verses of Ālamabanaparīkṣa in the form of syllogism to refute the various realist theories of atom (paramāṇu). Unfortunately, most of Kuiji's and his contemporary scholars' commentaries were lost in China and therefore not available to the Ming scholars. On the contrary, Xuanzang's Yogācāra heritage remained unbroken in Tokugawa Japan. Not surprisingly, both Kiben and Kaidō criticized the Ming Chinese commentaries for failing to properly understand the text and its logical arguments. This study concludes that a philosophical quest for the dialogue with realism was also shown in both Kiben's and Kaidō's works, which can be taken as a domestic clue to explain why modern European Buddhology and Indology had firmly taken root in the Meiji era without much resistance.