$omega$ Centauri (NGC 5139) hosts hundreds of pulsating variable stars of different types, thus representing a treasure trove for studies of their corresponding period-luminosity (PL) relations. Our goal in this study is to obtain the PL relations for RR Lyrae, and SX Phoenicis stars in the field of the cluster, based on high-quality, well-sampled light curves in the near-infrared (IR). $omega$ Centauri was observed using VIRCAM mounted on VISTA. A total of 42 epochs in $J$ and 100 epochs in $K_{rm S}$ were obtained, spanning 352 days. Point-spread function photometry was performed using DoPhot and DAOPHOT in the outer and inner regions of the cluster, respectively. Based on the comprehensive catalogue of near-IR light curves thus secured, PL relations were obtained for the different types of pulsators in the cluster, both in the $J$ and $K_{rm S}$ bands. This includes the first PL relations in the near-IR for fundamental-mode SX Phoenicis stars. The near-IR magnitudes and periods of Type II Cepheids and RR Lyrae stars were used to derive an updated true distance modulus to the cluster, with a resulting value of $(m-M)_0 = 13.708 pm 0.035 pm 0.10$ mag, where the error bars correspond to the adopted statistical and systematic errors, respectively. Adding the errors in quadrature, this is equivalent to a heliocentric distance of $5.52pm 0.27$ kpc.