Plumbing vent flashings are notorious spots for roof leaks. If you have a leak in the general area of a plumbing vent, check the condition of the vent flashing. Look for rust holes or gaps around metal vents (required for cast iron waste lines). If you have rubber vents (which are used for plastic pipe), check to see if they have become brittle and cracked.
Both types extend under at least two courses of shingles, so you'll usually need to remove a few shingles above the flashing to get the old one out without ripping any shingles. If you don't have any shingles left from the last roofing, be extra careful not to rip any. (Even if you can find new shingles in the same style, the color won't match perfectly.)
Loosen the tabs on the shingles above the vent first. Those shingles won't be removed, but you'll need to get under those tabs to get at the nails on the shingles directly below. Work from the top down, removing any shingles covering the vent flashing. Getting the tabs free without ripping them is the only tricky part. Work a putty knife slowly under the bottom lip of each tab and slip it through the adhesive to break the seal from one side to the other. Don't try to pry up the whole tab at once or it will rip. Once the tabs are free, slip the flat bar under the shingle and tap it up under the nail head. Pop the shingle and nail up, then pull the flat bar out from under the shingle and pop the nail head up from above the shingle. Don't worry if you accidentally tear the nail head through the shingle. When you replace the shingle, just put the nail in slightly above the hole and fill the old hole with caulk.
Slip a flat bar under the edge of the vent flashing and pop the nails up (Photo 1). Pull the old flashing up over the vent pipe and scrape any old caulk and debris off the roof. Slide the new flashing over the vent pipe and under the shingles above the pipe. Center the pipe in the flashing and push the flexible front corners up or down so that the flashing pipe is parallel to the vent pipe. (Rubber vent flashing automatically adjusts to any pitch.) Lift the vent enough to spread caulk under the sides (but not the bottom edge), then nail with three 1-1/4-in. roofing nails per side (Photo 2). Put one nail in the bottom edge with a dab of caulk under it to seal the hole.
Set the top part of the vent on the pipe. Make sure the inside of the lead collar fits inside the pipe, then tighten the pipe clamp. Finally, replace the shingles (Photo 3).