Should I reply to Editor of a journal after acceptance?
Is it common to thank the Editor after acceptance email?


It is uncommon, but this review was also an uncommon one.  From your description, it sounds like the Editor would have done a substantial amount of work considering the competing merits of conflicting reviews and your own rebuttal to a reviewer.  That is work in excess of what would normally occur in a review process, and so it would not be out of place to email and thank the Editor for his/her work.  It is nice to get thank-yous for doing your job well, so I would recommend you go with your instinct and send a thank-you email.