Abstract Dense gas in minihalos with masses of 10 6 −10 8 M ⊙ can shield themselves from reionization for ∼100 Myr after being exposed to the UV background. These self-shielded systems, often unresolved in cosmological simulations, can introduce strong absorption in quasar spectra. This paper is the first systematic study on the impact of these systems on the Ly α forest. We first derive the H i column density profile of photoevaporating minihalos by conducting 1D radiation–hydrodynamics simulations. We utilize these results to estimate the Ly α opacity from minihalos in a large-scale simulation that cannot resolve self-shielding. When the ionization rate of the background radiation is 0.03 × 10 −12 s −1 , as expected near the end of reionization at z ∼ 5.5, we find that the incidence rate of damped Ly α absorbers increases by a factor of ∼2−4 compared to at z = 4.5. The Ly α flux is, on average, suppressed by ∼3% of its mean due to minihalos. The absorption features enhance the 1D power spectrum up to ∼5% at k ∼ 0.1 h Mpc −1 (or 10 −3 km −1 s), which is comparable to the enhancement caused by inhomogeneous reionization. The flux is particularly suppressed in the vicinity of large halos along the line-of-sight direction at separations of up to 10 h −1 Mpc at r ⊥ ≲ 2 h −1 Mpc. However, these effects become much smaller for higher ionizing rates (≳0.3 × 10 −12 s −1 ) expected in the post-reionization Universe. Our findings highlight the need to consider minihalo absorption when interpreting the Ly α forest at z ≳ 5.5. Moreover, the sensitivity of these quantities to the ionizing background intensity can be exploited to constrain the intensity itself.