The DEEP-South (the Deep Ecliptic Patrol of the Southern Sky) photometric census of small Solar System bodies produces massive time-series data of variable, transient or moving objects as a by- product. To fully investigate unexplored variable phenomena, we present an application of multi-aperture photometry and FastBit indexing techniques for faster access to a portion of the DEEP-South year-one data. Our new pipeline is designed to perform automated point source detection, robust high-precision photometry and calibration of non-crowded fields which have overlap with previously surveyed areas. In this paper, we show some examples of catalog-based variability searches to find new variable stars and to recover targeted asteroids. We discover 21 new periodic variables with period ranging between 0.1 and 31 days, including four eclipsing binary systems (detached, over-contact, and ellipsoidal variables), one white dwarf/M dwarf pair candidate, and rotating variable stars. We also recover astrometry (< ±1–2 arcsec level accuracy) and photometry of two targeted near-earth asteroids, 2006 DZ169 and 1996 SK, along with the small- (0.12 mag) and relatively large-amplitude (0.5 mag) variations of their dominant rotational signals in R-band.