Acoustic signatures of the single-site quadrupolar Kondo effect in Y$_{0.966}$Pr$_{0.034}$Ir$_2$Zn$_{20}$ are presented. The elastic constant ($C_{11}-C_{12}$)/2, corresponding to the $Gamma_3$(E)-symmetry electric-quadrupolar response, reveals a logarithmic temperature dependence of the quadrupolar susceptibility in the low-magnetic-field region below $sim$0.3 K. Furthermore, the Curie-type divergence of the elastic constant down to $sim$1 K indicates that the Pr ions in this diluted system have a non-Kramers ground-state doublet. These observations evidence the single-site quadrupolar Kondo effect, as previously suggested based on specific-heat and electrical resistivity data.