We investigated the influence of stress on the acoustic wave propagation in single crystalline heterostructures using a transfer matrix method. Both Rayleigh-type and Sezawa modes exhibit an acoustoelastic anomaly, where the stress-induced change of the phase velocity is maximum for finite film thicknesses, considerably smaller than the acoustic wavelength. For Ge/Si͑001͒ compressed by 1 GPa the velocity shift of Sezawa modes reaches exceptionally high values of about 2%. These results demonstrate the importance of stress effects on the determination of elastic constants of thin film heterostructures.