Glyphosate, the most applied herbicide globally, offers effective non-selective and post-emergent weed control. Evolution of herbicide-resistant weeds is commonly associated with the recurrent application of herbicides with the same mode of action. Native to South America, hairy fleabane (Erigeron bonariensis L.) is the most problematic weed in this sub-continent and has previously been confirmed glyphosate resistant. This research aimed at characterizing glyphosate-resistant populations, thus estimating the frequency of resistance, resistance levels and identifying effective herbicide alternatives to control glyphosate-resistant populations. Glyphosate resistance characterization was initially conducted on ten suspected populations collected in plantain, banana, cassava, passionfruit, papaya, and drybean crops. Two resistant populations were selected and further characterized through dose-response tests; in addition, response to alternative herbicides (paraquat, glufosinate, 2,4-D, pyraflufen-ethyl, and mesotrione) was determined. All surveyed hairy fleabane populations survived (≥80% of individuals) the recommended glyphosate rate of 1080 g ae ha−1; conversely, five populations collected from non-cropping areas were effectively controlled at this same rate. Dose-response tests estimated resistance factors of 3.15- to 22.3-fold versus the most susceptible population. Interestingly, resistance profile and dose-response tests detected hormesis responses at field-recommended rates. The most effective herbicide alternatives to control glyphosate-resistant hairy fleabane were pyraflufen-ethyl and mesotrione.