The Pole was beaten by Jelena Ostapenko in the US Open fourth round last week, a defeat which meant Aryna Sabalenka of Belarus took over as the top-ranked player.
Swiatek had said she needed a reset after her 75-week run as world number one came to an end.
"Unfortunately I need to withdraw from the tournament in Guadalajara due to a change of schedule," Swiatek posted on social media platform X.
"I need to listen to my body and the season is very intense - our number one priority is to play it until the end in good health and plan it wisely so we wouldn't risk an injury."
French Open champion Swiatek, who was set to make her debut in the September 17th-23rd Guadalajara tournament, said she would return to action in Tokyo at the start of next month.
US Open champion Coco Gauff, defending Guadalajara champion Jessica Pegula, 2022 runner-up Maria Sakkari and Tunisia's Ons Jabeur have all entered the Mexico event.
