The venerable Slater, 41, narrowly defeated 21-ear-old Hawaiian hometown favorite John Florence in the final heat of the tournament, which closed out the Association of Surfing Professionals season.
Slater and Florence navigated towering 10-to-15-foot waves on Oahu's famed North Shore and came away with a 16.37-15.90 victory.
Slater also put to rest speculation that 2013 would be his final season on the pro circuit. "Today is a day I have dreamed about since I was a little kid – big, perfect, West-angled Pipeline and a showdown at the Pipe Masters," he said. "I want more days like this so I'm definitely back next year."
Saturday marked Slater's seventh title at the Billabong Pipe Masters and 56th ASP world tour win.
The Pipe Masters had earlier determined the ASP men's champion for the season. Mick Fanning captured the title in the quarterfinals against fellow Australian Yadin Nicol, but then lost in the semis to Florence.