Brown rot (Phomopsis vexans) is a destructive disease of eggplant, which mainly causes fruit rot. It is currently managed through extensive foliar applications of fungicides, such as benzimidazole chemicals. In this research study, a total of 513 single-conidial isolates of P. vexans were collected between 2010 and 2013 for the purpose of characterizing their resistance to benzimidazole fungicides and diethofencarb. Two types of benzimidazole-resistant (Ben R) isolates, Ben R1 (benzimidazole-resistant and diethofencarb-sensitive), and Ben R2 (benzimidazole-resistant and diethofencarb-resistant), were detected. Ben R1 was associated with a point mutation from the GAG to GTG at codon 198 in the β-tubulin gene of the Ben S isolates, and was predicted to cause changes from glutamic acid to valine. Ben R2 was associated with a point mutation from the TTC to TAC at codon 200 in the β-tubulin gene of the Ben S isolates. It was determined that, whether the isolates of the P. vexans were sensitive or resistant to the benzimidazole fungicides, pyraclostrobin (a QoI fungicide) showed strong bioactivity against their mycelial growth, spore germination, and disease lesion development. Also, experiments in 2014 and 2015 at three testing sites showed that pyraclostrobin provided excellent control against brown rot disease in the eggplant fields, and significantly increased the yields of the eggplant fruits. Meanwhile, the applications of benzimidazole fungicides (carbendazim alone or mixed with diethofencarb) were found to aggravate the occurrences of the brown rot, and the eggplant yields were observed to decrease. The baseline sensitivity of the P. vexans to pyraclostrobin was further determined for these 513 isolates. In regard to inhibiting the mycelial growth, the mean EC50 values of the tested isolates were determined to be 3.19 ± 0.43 and 1.28 ± 0.14 mg l−1, respectively, in the absence and presence of the alternative oxidase specific inhibitor salicylhydroxamic acid (SHAM), and the range-of-variation factors were 49.6 and 35.1. For inhibiting spore germination, the mean EC50 values were 0.61 ± 0.12 and 0.39 ± 0.11 mg l−1, with the range-of-variation factors of 32.1 and 17.9, respectively. This study confirmed a serious resistance emergency to benzimidazole fungicides in the P. vexans populations, and indicated that pyraclostrobin may be a good alternative fungicide to control eggplant brown rot.