A two-microphone transfer function (TMTF) method is adapted to a numerical framework to compute the radiation and input impedances of three-dimensional vocal tracts of elliptical cross-section. In its simplest version, the TMTF method only requires measuring the acoustic pressure at two points in an impedance duct and the postprocessing of the corresponding transfer function. However, some considerations are to be taken into account when using the TMTF method in the numerical context, which constitute the main objective of this paper. In particular, the importance of including absorption at the impedance duct walls to avoid lengthy numerical simulations is discussed and analytical complex axial wave numbers for elliptical ducts are derived for this purpose. It is also shown how the direct impedance of plane wave propagation can be computed beyond the TMTF maximum threshold frequency by appropriate location of the virtual microphones. Virtual microphone spacing is also discussed on the basis of the so-called singularity factor. Numerical examples include the computation of the radiation impedance of vowels /a/, /i/, and /u/ and the input impedance of vowel /a/, for simplified vocal tracts of circular and elliptical cross-sections.