Stosur set up the clash with the 2016 Australian Open champion and Wimbledon finalist with a second round straight sets win over Japan’s Misaki Doi 6-3 6-4.
The top-seeded Australian started strongly against Doi, who is ranked world No.38, and said the swirling conditions on the Rio courts again made play tough.
She stumbled early in the second and trailed 0-3 but was able to regain control and level at 3-3 before wrapping up the win.
Kerber booked her third round berth with a convincing win over Canada’s Eugenie Bouchard but Stosur said she felt she matched up well, with the pair three wins apiece.
The Australian world No.17’s last win over Kerber came in Madrid last year.
“It’s going to be hard as she’s the second best player in the world and she’s won a grand slam and made the final of another and she’s playing really well at the moment,” Stosur said.
“I’ve had success against her in the past and I know I’m going to have to play some very good tennis to win.
“I fully believe I can win this match and I’m going to go out there and give it everything I can.”
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