Sclerotinia sclerotiorum, a pathogen of more than 600 host plants, secretes oxalic acid to regulate the ambient acidity and provide conducive environment for pathogenicity and reproduction. Few Aspergillus spp. were previously proposed as potential biocontrol agents for S. sclerotiorum as they deteriorate sclerotia and prevent pathogen’s overwintering and initial infections. We studied the nature of physical and biochemical interactions between Aspergillus and Sclerotinia. Aspergillus species inhibited sclerotial germination as they colonized its rind layer. However, Aspergillus-infested sclerotia remain solid and viable for vegetative and carpogenic germination, indicating that Aspergillus infestation is superficial. Aspergillus spp. of section Nigri (Aspergillus japonicus and Aspergillus niger) were also capable of suppressing sclerotial formation by S. sclerotiorum on agar plates. Their culture filtrate contained high levels of oxalic, citric and glutaric acids comparing to the other Aspergillus spp. tested. Exogenous supplementation of oxalic acid altered growth and reproduction of S. sclerotiorum at low concentrations. Inhibitory concentrations of oxalic acid displayed lower pH values comparing to their parallel concentrations of other organic acids. Thus, S. sclerotiorum growth and reproduction are sensitive to the ambient oxalic acid fluctuations and the environmental acidity. Together, Aspergillus species parasitize colonies of Sclerotinia and prevent sclerotial formation through their acidic secretions.