Both sentences are correct, but the meaning is different. With the first, you are saying *you* pulled out the tooth (your tooth or someone else's) and not the dentist.The 2nd is probably what you mean - a dentist pulled out your tooth yesterday. "I had a root canal" or "I had a root canal done" is when a dentist does the procedure for you (I hope !) "I did a root canal" is when you performed the procedure. Not likely :) .... unless you are a dentist and you are describing a procedure you did.

Hi Amirhossein, I agree with Greg, and just want to add that “I had a tooth pulled”, with no phrasal particle, is most natural for the meaning described.