Time for a new flashing boot. Carefully remove the shingles around the area with a shingle pry bar and you can use them again. Remove the plumbing boot and clean off all that old caulking so the pipe is smooth. Install a new flashing boot, reinstall the shingles and hand seal down the shingles along the old seal strip. Not a dificult repair IF you are comfortable on the roof. Also, while you have the shingles off, sand down the pipe to get the loose stuff off and hit it with a coat of paint to slow down the rusting.
And, welcome to House Repair Talk!