Kerber netted a forehand down the line to reach deuce before mounting baseline pressure from Williams resulted in a break of serve to reach 3-5.
Williams held serve, then broke serve before holding serve again to lead 6-5 after winning five total games in a row.
Serving to stay in the set, Kerber faced another set point which she erased before hitting a forehand down the line to game point winner to enter the tiebreaker.
Williams took a 5-0 lead in the tiebreaker following several unforced errors from Kerber.
A Kerber crosscourt forehand winner drew the score to 5-1 before the German would hit a crosscourt backhand long to fall behind 1-6 and face another set point.
A 113 miles per hour Williams ace out wide put the American ahead by one set.
In set two, Williams held serve then broke serve to take a 2-0 lead.
Serving down a break at 3-5, Kerber netted a crosscourt forehand followed by two backhands to face match point at 0-40.
The German saved all three match points before hitting a crosscourt forehand long to end the match.
Williams is next scheduled to compete this week at the Rogers Cup in Montreal, Canada.