The ninth-seeded Wozniacki, who has never fared very well on the London grass, is going through a mediocre season. She also lost in the 2nd round at the French Open.
The 196th-ranked Cetkovska, who reached the fourth round at Wimbledon two years ago, erased the six break points she faced and hit 30 winners.
A qualifier from the Czech Republic, Cetkovska's 2012 was cut short after the London Olympics because of a right ankle injury. She returned this year and has nosedived in the WTA rankings.
Results from the third day of Wimbledon (x denotes seeded player):
Men's singles:
Second round:
Lukasz Kubot (POL) bt Steve Darcis (BEL) - walkover
Adrian Mannarino (FRA) bt John Isner (USA x18) 1-1 - retired
Jerzy Janowicz (POL x24) bt Radek Stepanek (CZE) 6-2, 5-3 - retired
Viktor Troicki (SRB) bt Andrey Kuznetsov (RUS) 6-4, 6-3, 6-4
Lukosz Kubot (POL) bt Steve Darcis (BEL) - walkover
Kenny de Schepper (FRA) bt Marin Cilic (CRO x10) - walkover
Women's singles:
Second round:
Monica Puig (PUR) bt Silvia Soler (ESP) 6-2, 5-7, 6-4
Carla Suarez Navarro (ESP x19) bt Mirjana Lucic (CRO) 1-6, 6-3, 6-3
Alize Cornet (FRA x29) bt Su-Wei Hsieh (TPE) 6-3, 6-2
Flavia Pennetta (ITA) bt Victoria Azarenka (BLR x2) - walkover