The current research investigates the magnetohydrodynamic (MHD) slip flow of second-grade nanofluids past a permeable stretching sheet in a porous medium. The flow analysis is accomplished considering thermophoresis, Brownian diffusion, chemical reaction, and elastic deformation. The implementation of the Modified Buongiorno model (MBM) on second-grade nanofluid is the novel aspect of the study. The formulated coupled nonlinear equations are non-dimensionalized, applying suitable similarity transformation. Numerical resolution of the resulting equations is achieved via MATLAB solver bvp4c. In our problem, two different groups of nanofluids, $Cu-EO$ and $TiO_2-EO$, have been considered. The development of profiles of nanofluid velocity, temperature, concentration, entropy generation and Bejan number, with the flow parameters, is elaborated graphically. Tabulated values of skin friction, Nusselt number, and Sherwood number are illustrated. The principal outcomes of this study demonstrate a higher rate of heat transfer of $Cu-EO$ nanofluid than $TiO_2-EO$ nanofluid. The Nusselt number significantly decelerates, and the Sherwood number accelerates due to the combined influence of the Brownian diffusion and thermophoresis parameters. The second-grade parameter and nanoparticle volume fraction boost the skin friction magnitude. Furthermore, the entropy generation increases due to the Brinkman number and concentration diffusion parameter. The present research can be utilized to enhance the effectiveness of cooling systems in automobile engines, nuclear reactors, and heat exchangers. For the validation of our result, a comparative study is made with the previous authors and concludes in good agreement.