Clean the area around the flashing hole with a wire brush. The brush not only removes any dirt and debris around the hole, which allows the roof cement to adhere more effectively, it also abrades the surface. Wipe away the sanding dust with a tack cloth.
Measure the damaged area and add 4 inches to the number. Slip on a pair of work gloves and safety goggles before cutting out a piece of aluminum or galvanized steel according to this measurement with tin snips. Use the same product your flashing is constructed from.
Wipe down the flashing with a rag to remove any lingering dust, and cover the area around the damage with a heavy layer of roofing cement. Center the metal patch over the hole and press it down into the roofing cement.
Cover the edges of the patch with another heavy layer of roofing cement to create a water-tight seal. The drying time for the cement depends on its manufacturer, the air temperature, the flashing's surface temperature, humidity and wind.