Photovoltaic mounting systems that form chemical flashings are provided herein. Such sealant injection systems provide directional control and containment of sealant flow to form a chemical flashing that improves sealing of roof penetrations. Such systems can include a base assembly adapted to mount to a roof surface and support a mounting bracket having a photovoltaic module coupling device. The base assembly can include a sealant guide, a compressing plate and a sealant cartridge held between the guide and compressing plate by one or more coupling features of the guide. The coupling features can include a first set of features, such as a series of tabs, that facilitate coupling between the guide and the compressing plate. The base assembly can further include a base that releasably couples to the sealant guide by a second set of coupling features. Methods of mounting such base assemblies on roof surfaces are also provided.