In this work, the magnetohydrodynamic flow of two engine oil-based second-grade nanofluids Copper ($Cu$) and Titanium oxide ($TiO_2$) over a penetrable stretching sheet is studied. The flow, heat and mass transfer characteristics in the existence of activation energy, inclined magnetic field, Brownian diffusion, elastic deformation, and thermophoresis are examined. The coupled nonlinear model equations are formulated by implementing the Modified Buongiorno model and then are non-dimensionalized by the similarity transformation technique. The non-dimensional equations are simulated numerically using the bvp4c solver. Graphs are plotted to study the flow behaviour of nanofluid with the rate of entropy generation and Bejan number. The outcomes of skin friction coefficient, Nusselt number and Sherwood number are exhibited via surface plots. From the analysis, a higher inclination of the magnetic field decays the velocity and amplifies the temperature profiles. The heat transport rate diminishes with the Brownian diffusion, thermophoresis and elastic deformation parameters. The mass transport rate is accelerated due to the activation energy parameter. The entropy generation rate is enhanced with the Brinkman, Biot and local Reynolds numbers. Furthermore, it is seen that engine oil-based $TiO_2$ nanofluid has larger velocity, temperature and rate of entropy generation than engine oil-based $Cu$ nanofluid. The current examination has applications in automobile radiators, microchips, biomedical engineering, and extraction of geothermal power.