The Cougars built a 22-7 lead, only to see the 26-time champion Golden Bears storm back to cut the deficit to 22-19.
But BYU took over after that outscoring cal 21-7 to pull away for the victory.
"Our goal at the start of the year was to win a Varsity Cup national championship, and our boys did it, so that’s where we feel we’re at," said BYU coach David Smyth.
"There’s a tradition here," said senior Kyle Sumsion. "That’s what we play for."
This was the 9th straight championship game for BYU and third straight title. The Cougars finished the season with a record of 18-1.