SrTiO3 (STO) is a versatile substrate with a high dielectric constant, which may be used in heterostructures with 2D materials, such as MoS2, to induce interesting changes to the electronic structure. STO single crystal substrates have previously been shown to support the growth of well-defined epitaxial single-layer (SL) MoS2 crystals. The STO substrate is already known to renormalize the electronic bandgap of SL MoS2, but the electronic nature of the interface and its dependence on epitaxy are still unclear. Herein, we have investigated an in-situ physical vapor deposition (PVD) method, which could eliminate the need for ambient transfer between substrate preparation, subsequent MoS2 growth and surface characterization. Based on this, we then investigate the structure and epitaxial alignment of pristine SL MoS2 in various surface coverages grown on two STO substrates with a different initial surface lattice, the STO(001)(4 × 2) and STO(111)-(9/5 × 9/5) reconstructed surfaces, respectively. Scanning tunneling microscopy shows that epitaxial alignment of the SL MoS2 is present for both systems, reflected by orientation of MoS2 edges and a distinct moiré pattern visible on the MoS2(0001) basal place. Upon increasing the SL MoS2 coverage, the presence of four distinct rotational domains on the STO(001) substrate, whilst only two on STO(111), is seen to control the possibilities for the formation of coherent MoS2 domains with the same orientation. The presented methodology relies on standard PVD in ultra-high vacuum and it may be extended to other systems to help explore pristine two-dimensional transition metal dichalcogenide/STO systems in general.