The world No. 1 Williams improved to 27-1 this year by coming from behind to beat game German Anna-Lena Friedsam 5-7, 6-3, 6-3 on Court Lenglen.
Williams is a 19-time Grand Slam champion who owns two French Open titles (2002, 2013). She currently holds the Australian and U.S. Open crowns.
Kvitova, meanwhile, hasn't had much success on the famed red clay at Roland Garros, with five losses prior to the quarterfinals in six previous appearances. She needed three sets to win her first-round match on Tuesday and again went the distance on Day 5.
The two-time Wimbledon champ survived with a 6-7 (4-7), 6-4, 6-2 victory over Spain's Silvia Soler-Espinoza to advance to the third round. Despite her troubles in the French capital, the fourth-seeded Kvitova did enter this year's second major with some solid results on the slow surface, winning the Madrid Open before a quarterfinal appearance in Rome.
Next up for Kvitova will be 30th-seeded Romanian Irina-Camelia Begu, who rolled to a 6-2, 6-0 victory over Croatia's Ana Konjuh.
The 2014 U.S. Open runner-up Wozniacki has struggled even more than Kvitova in Paris and again made an early exit with a 6-4, 7-6 (7-4) loss against Germany's Julia Goerges.
The fifth-seeded Dane has been past the third round only once in nine visits to Roland Garros -- a quarterfinal result in 2010. She was a first-round loser last year and departed in the second round in 2013.
With Wozniacki's exit, the women's draw has now lost three of the top-six seeds, including No. 3 Simona Halep and No. 6 Genie Bouchard.
Goerges, who has never advanced beyond the fourth round in any of her previous 28 Grand Slam events, will play American Irina Falconi in the third round. Falconi advanced with a 3-6, 6-1, 6-2 triumph over Bulgaria's Sesil Karatantcheva.
Tenth-seeded German Andrea Petkovic rallied for a 4-6, 6-4, 6-4 win over Spain's Lourdes Dominguez Lino and will next play 17th-seeded former French Open runner-up Sara Errani, who also needed three sets to dispose of Germany's Carina Witthoeft, 6-3, 4-6, 6-2.
Also on Thursday, Romanian Andreea Mitu surprised 12th-seeded Czech Karolina Pliskova 2-6, 7-6 (7-5), 6-4 and in a battle of former French Open champs, Italian Francesca Schiavone outlasted 18th-seeded Russian Svetlana Kuznetsova 6-7 (11-13), 7-5, 10-8.