The top-seeded American, playing her first tournament since a disappointing Wimbledon campaign in which she was slowed by a virus, got her hardcourt build-up to the US Open off to a good start and will try to carry the momentum into next week's tournament at Montreal.
Williams collected her third Stanford trophy and her fourth title of 2014, after triumphs in Brisbane, Miami and Rome.
But the 17-time Grand Slam champion has struggled in majors this year, failing to make it past the fourth round in the Australian Open, French Open or Wimbledon.
She'll have her last chance of the year to add another major title to her resume at the US Open, which starts at Flushing Meadows on August 25.
Kerber, who saved a match point en route to her semi-final victory over Varvara Lepchenko on Saturday, leapt to a 5-1 lead in the opening set.
Trailing 5-2, Williams saved two set points as she broke Kerber to trim the gap to 5-3, part of a run of five straight games that gave her a 6-5 lead.
Kerber saved a set point in the next game as she held serve to force a tiebreaker that an increasingly confident Williams dominated.
Williams broke Kerber to open the second set and led the rest of the way, although she needed four match points to finally put the match away.