In Saccharomyces cerevisiae, the iron-sulfur cluster biogenesis late-acting subsystem (Fe-S-IBG) comprises the mitochondrial glutaredoxin (Grx5), Isa1, Isa2, and iron-sulfur cluster assembly factor IBA57 (Iba57) proteins. The Fe-S-IBG subsystem assists in inserting [4Fe-4S] clusters into apoproteins, some of which belong to the electron transport chain (ETC). However, whether the Fe-S-IBG subsystem indirectly stabilizes respiratory supercomplexes and proper ETC function via insertion of [Fe-S] proteins into ETC complexes remains to be elucidated. We compared the effects of ISA2- and GRX5-independent mutations on the insertion of Rip1p, a [2Fe-2S]-containing protein involved in both electron transfer in the bc1 complex and the formation of respiratory supercomplexes. The levels of Rip1p, supercomplex assembly, ETC function, oxidative stress, and resistance of yeast to ethanol stress were evaluated on haploid S. cerevisiae cells with independent mutations of the ISA2 and GRX5 genes. Susceptibility to ethanol was increased in the isa2Δ and grx5Δ mutants, which was associated with enhanced glutathione oxidation due to higher levels of free iron and increased oxidants. Furthermore, the isa2Δ mutant showed decreased Rip1p expression, respiratory dysfunction, and defective respiratory supercomplex formation, which was restored by ISA2 complementation. These results suggest that Isa2p is essential for proper respiratory chain function and resistance to oxidative stress by stabilizing supercomplexes in a manner dependent on Rip1p insertion in the cytochrome bc1 complex.