Based on 2.93 fb$^{-1}$ $e^+e^-$ collision data taken at center-of-mass energy of 3.773 GeV by the BESIII detector, we report searches for the singly Cabibbo-suppressed decays $D^{+}toomegapi^{+}$ and $D^{0}toomegapi^{0}$. A double tag technique is used to measure the absolute branching fractions $mathcal{B}(D^{+}toomegapi^{+})=(2.79pm0.57pm0.16)times 10^{-4}$ and $mathcal{B}(D^{0}toomegapi^{0})=(1.17pm0.34pm0.07)times 10^{-4}$, with statistical significances of $5.5sigma$ and $4.1sigma$, respectively. We also present measurements of the absolute branching fractions for the related $eta pi$ decay modes. We find $mathcal{B}(D^{+}toetapi^{+})=(3.07pm0.22pm0.13)times10^{-3}$ and $mathcal{B}(D^{0}toetapi^{0})=(0.65pm0.09pm0.04)times10^{-3}$, which are consistent with the current world averages. The first and second uncertainties are statistical and systematic, respectively.