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Yes, you can use an asphalt-based caulk around where the pipe 'meets' the flashing. I usually go up on my roof once a year (when I have the ladder out) to inspect my chimmney and stacks.
Visit you local Home Center for the asphalt caulk. Make sure it's REAL dry when you apply it. Also, you'll want to kinda 'smear' the caulk around a little to work it into any grooves or cracks you caulk. And be careful not to break any shingles.
Oh, my assumptions: You have asphalt/fiberglass shingles, and you're 'comfortable' in your mind to go up on the roof.
At worst, you can replace the 'cowl' that goes over the pipe if it still leaks. And while you're up there too, put a dab or 2 under the surrounding shingles (and press down) to keep those shingles down in a strong wind (especially while it's raining.)
My best to ya and hope this helps.
Jay J -Moderator