Plumbing DWV isometric drawing tool (free or <= $40)

If you have access to the underside of the roof, removing the pipe and reconstructing the roofing is not difficult. Such a repaired roof is much less likely to leak than with the pipe sticking through over the years.

By the number of steps, this might seem daunting, but each is very simple and an intuitive step in a lasting, trouble-free repair.

The basics are removing the bad stuff, repairing the hole, and renewing the roofing to make it weather tight.

1. After removing the pipe and flashing, clean up the hole through the roof decking, possibly called cladding or sheathing, (assuming the roof is not wooden shake or shingles) by cutting through with a hand saw, jig saw, or judicious use of a circular saw and make the hole rectangular (if not already).

2. Working from underneath, cut a piece of plywood of the same thickness as the decking to fit inside the hole to make a filler piece for the decking/sheathing/cladding.

3. Create support for the filler piece by cutting some more plywood, or a 1x4 (maybe two) to fit snugly between the roof joists and fasten into place by screwing/nailing through the joists into the plywood or board supports.

4. Topside, fasten the decking filler to the supporting layer: construction glue, short nails, or screws. It just needs to be strong enough to shrug off walking on the roof.

5. Peel back and remove a row or two of roofing to access the tar paper and make it so a nice new piece of roofing fits cleanly. At the up-slope edge of the row above, try to loosen and remove the roofing nails holding the shingles with a wide flat-blade screwdriver or thin pry bar instead of simply ripping the roofing material. If there is more than one layer of shingles (up to three layers are allowed), forget going for the tar paper: instead, make some "roofing filler" with scrap shingles and fill in the hole in the roofing to make a consistent support surface for the "finish layer" of roofing.

6. Obtain new tar paper and roof shingles. Probably you will have to buy roofing in units of 33 square feet (1/3 of a "square") and tar paper in obscenely long rolls. It might pay to go to a local hardware store to see if they will sell it by the foot. Maybe you want to use it up a whole package of roofing by replacing more of the roofing. If so, remove roofing up to the first ridge or peak.

7. If the old tar paper is exposed, Add new tar paper by tucking it under shingles above and at sides and lightly tacking it down with a few short staples. Cut off the excess, but keep 6 inches over the lower row of shingles (down to just above the tar strip).

8. Working from the bottom, follow the existing pattern of shingle placement and overlap. Usually each row is 1/3 to 1/2 offset of the width of a shingle to stagger the side joints (to protect it by the next row above). Place nails 1/2 inch upslope from the tar strip (black goo stuff near the middle of the shingle). A maximum of three nails per shingle is all that is needed. The next row will add up to three more nail fastenings which is plenty of holding power. The black goo will melt on the next hot day to secure the shingles together.

9. At the top where the new roofing joins the existing, slide the new roof shingles under the existing row and gain access to the nailing strip by gently lifting and curling the lower edge of the row above it. Nail carefully.

10. If there is any doubt about an exposed seam, use a suitable roof patch caulk. If doing this during cold weather and it will not be warm before the next wind storm, it might be worth judicious use of a torch (directed flame) to heat the lower edge of the shingles to get them to stick together a little. Given time, they will adhere on their own adequately.

The smaller diameter pipe is because it is specified for in-wall use. The socket end of a standard 3" PVC pipe coupling is 3.97" which is wider than a 2 x 4 stud wall cavity, which is 3.5". The 3.25" pipe OD on the in-wall pipe allows for a smaller coupling which can fit inside the wall cavity.

Depending on the size and type of leak, you might have been able to seal it up without having to cut it out. I put a nail for a picture frame through a drain line once. To repair it, I scraped some shavings from some scrap PVC, mixed it with a little bit of PVC solvent until it formed a paste and then filled the nail hole with it. Note, that I would never do this on a pressurized line.