We present a new method to effectively select objects which may be low-mass active black holes (BHs) at galaxy centers using high-cadence optical imaging data, and our first spectroscopic identification of an active 2.7x10^6 Msun BH at z=0.164. This active BH was originally selected due to its rapid optical variability, from a few hours to a day, based on Subaru Hyper Suprime-Cam~(HSC) g-band imaging data taken with 1-hour cadence. Broad and narrow H-alpha and many other emission lines are detected in our optical spectra taken with Subaru FOCAS, and the BH mass is measured via the broad H-alpha emission line width (1,880 km s^{-1}) and luminosity (4.2x10^{40} erg s^{-1}) after careful correction for the atmospheric absorption around 7,580-7,720A. We measure the Eddington ratio to be as low as 0.05, considerably smaller than those in a previous SDSS sample with similar BH mass and redshift, which indicates one of the strong potentials of our Subaru survey. The g-r color and morphology of the extended component indicate that the host galaxy is a star-forming galaxy. We also show effectiveness of our variability selection for low-mass active BHs.