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This study proposes a two-photomask process for fabricating amorphous indium–gallium–zinc oxide (a-IGZO) thin-film transistors (TFTs) that exhibit a self-aligned structure. The fabricated TFTs, which lack etching-stop (ES) layers, have undamaged a-IGZO active layers that facilitate superior performance. In addition, we demonstrate a bilayer passivation method that uses a polytetrafluoroethylene (Teflon) and SiO2 combination layer for improving the electrical reliability of the fabricated TFTs. Teflon was deposited as a buffer layer through thermal evaporation. The Teflon layer exhibited favorable compatibility with the underlying IGZO channel layer and effectively protected the a-IGZO TFTs from plasma damage during SiO2 deposition, resulting in a negligible initial performance drop in the a-IGZO TFTs. Compared with passivation-free a-IGZO TFTs, passivated TFTs exhibited superior stability even after 168 h of aging under ambient air at 95% relative humidity.