Lean the ladder against the roof overhang. Make sure the ladder is stable before climbing onto the roof.
Pull back the shingles covering the pipe boot. Pry them from the roof with the claw end of your hammer if pulling them back doesn't give you enough access.
Pry away the nails holding the existing boot in place, before sliding the boot up and off the vent pipe. The vent pipe will not be much longer than 12 inches, so sliding the boot over the pipe will not be difficult.
Scrape away any caulk or roofing tar on the vent pipe or on the decking (wood beneath the roofing shingles) with the putty knife. Lumps and debris will reduce the integrity of your new seal.
Slide the new boot down the vent pipe until the bottom is against the decking. Nail it to the decking, and squeeze a bead of caulk around the seam where the boot meets the decking. Squeeze another bead around the seam where the top of the boot meets the pipe.
Press the shingles back down, or nail on new ones if you had to remove the original shingles.