Plumbing vent pipes on house roofs are covered with a metal square of flashing and sealed with silicone caulking.
How to seal reaeal pipe boot on roof.
How to seal a plumbing vent pipe on the roof.
Even if the hole matches the size of the pipe perfectly there will still be gaps.
The slide the boot down the pipe and leave it about 3 above the roof.
And begging to caulk around where the boot will go on the roof.
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This is why they re installed with a rubber boot.
Find quality vent pipe flashing online or in store.
Now slide the boot down and make sure there is enough caulk to have a seamless circle all the way around.
These gaps should be sealed.
On the boots if you have metal roof jacks with rubber boot seals on top with many models the rubber seals can be popped off and replaced without removing the metal part and there are also slip over boots that can just nestle down over the existing damaged boot and overlap the top of the jack but contractor would have to look at it and see then go get parts so if using a contractor.
Place the new boot in the hole of the pipe and cut the boot on the line that touches the rim.
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The flashing of the vent pipes.