Photovoltaic mounting systems having sealant injection system are provided herein. Such sealant injection systems provide improved directional control of sealant flow and improved sealing of roof penetrations during mounting with one or more fasteners. Such systems can include a bracket assembly having a removable sealant injection package. The sealant injection package includes a collapsible sealant injection reservoir and is adapted to provide directionally controlled release of sealant upon collapse. Such a system can further include sealant injection guides that direct flow of sealant during mounting and pads or caps that cover and enclose the injected sealant so as to ensure adequate sealing of any roof penetrations and maintain its integrity over time. Such systems further allow for sealant injection packages to be interchanged or replaced as needed and allow for ready removal or replacement of the bracket after mounting while maintaining the seal of any roof penetrations.