We report on a deep XMM-Newton EPIC observation of the globular cluster Omega Cen performed on August 13th, 2001. We have detected 11 and 27 faint X-ray sources in the core and half mass radii, searching down to a luminosity of 1.3 x 10(31) ergs s(-1) in the 0.5- 5 keV range. Most sources have bolometric X-ray luminosities between similar to10(31)-10(32) ergs s(-1). We present the color-color and hardness-intensity diagrams of the source sample, as well as high-quality EPIC spectra of the brightest objects of the field, including the two candidate Cataclysmic Variables (CVs) in the core and the quiescent neutron star low-mass X-ray binary candidate. The spectra of the latter objects fully support their previous classification. We show that the bulk of sources are hard and spectrally similar to CVs. The lack of soft faint sources might be related to the absence of millisecond pulsars in the cluster. The XMM-Newton observations reveal the presence of an excess of sources well outside the core of the cluster where several RS CVn binaries have already been found. We have also analyzed a publicly available Chandra ACIS-I observation performed on January 24-25th, 2000, to improve the XMM-Newton source positions and to search for source intensity variations between the two data sets. 63 XMM-Newton sources have a Chandra counterpart, and 15 sources within the half-mass radius have shown time variability. Overall, the general properties of the faint X-ray sources in omega Cen suggest that they are predominantly CVs and active binaries (RS CVn or BY Dra).