The pair exchanged breaks in each other's first service games before the German's superiority began to tell.
Kerber was returning serve excellently, forcing Keys into a number of errors.
The American conjured some fantastic shots, hitting a total of 13 winners during the first set.
However, Kerber's consistency allowed her to take it 6-2.
The second set began in the same way as the first, with both players breaking at the first attempt.
Kerber always looked in control of the contest, but Keys was scrapping for every point.
The 17-year-old held her own until losing a pivotal game at 5-5, which gave her opponent the opportunity to serve for a place in the fourth round.
Keys was going out all guns blazing and earned herself two break points as Kerber looked as if she was flinching at the vital moment.
A big forehand helped fifth seed to steady the nerves, before Keys dumped into the net to bring up deuce.