We examine the effect of interface disorder in suppressing superconductivity in coherently grown ultrathin YBa${}_{2}$Cu${}_{3}$O${}_{7}$ (YBCO) layers on SrTiO${}_{3}$ (STO) in YBCO/STO superlattices. The termination plane of the STO is TiO${}_{2}$ and the CuO chains are missing at the interface. Disorder (steps) at the STO interface cause alterations of the stacking sequence of the intracell YBCO atomic layers. Stacking faults give rise to antiphase boundaries which break the continuity of the CuO${}_{2}$ planes and depress superconductivity. We show that superconductivity is directly controlled by interface disorder outlining the importance of pair breaking and localization by disorder in ultrathin layers.