Parkinson, 31, outscored Kerr 17.17-14.83 to win the venerable North Shore tournament and also clinch the Association of Surfing Professionals World Championship Tour title for 2012.
Parkinson's bid for the ASP crown came down to the final heat of the Billabong. American Kelly Slater was the only other competitor with a shot but he lost to Kerr in the semifinals.
"I figured it was going to be a pressure cooker like a few years ago," said Parkinson, who was runner-up in the ASP race last year. "I knew there was nothing I could do about it. It was about what I had to do."
Kerr, who competed despite nerve damage suffered in a spill in an earlier heat, finished No. 8 in the world rankings.