The loss for third seed Williams extended a disappointing season so far for the seven-times grand slam champion as she arrived on the unique green clay courts of Charleston having lost her opening match in four of five previous events.
Williams was plagued by errors during a breezy first set, misjudging several volleys and overheads, while Putintseva used her backhand drop-shot to perfection on key points even when pinned deep in the court.
Putintseva, who earned her first victory in four career meetings against Williams, will next face fifth seed Sara Errani after the Italian beat 10th-seeded Australian Samantha Stosur 6-4 7-6(5).
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Kerber had no trouble with the wind as she recorded 35 winners and converted seven of her 10 break points to get by Kucova in 85 minutes.
"I think the feeling is coming back from last year because right now I'm feeling much better on clay again," said the German.
Kerber kicks off the action on Friday versus Romanian Irina-Camelia Begu, who advanced with a 1-6 6-2 7-6(4) win over Puerto Rico's Monica Puig.
(Reporting by Frank Pingue in Toronto; Editing by Larry Fine/Peter Rutherford)
