Suarez Navarro needed to make the final in Russia to overtake the Czech and book a spot in the elite tournament in Singapore, which starts on Sunday, but was beaten by Russia's Daria Kasatkina 6-1 6-2 in her last eight clash.
Safarova, who had already qualified for the WTA Finals doubles with partner Bethanie Mattek-Sands, will make her debut in the tournament after a standout year where she reached the final of the French Open.
She also won the Australian Open and French Open doubles titles with the American.
"I am really excited to qualify for the WTA Finals for the first time," Safarova, the world number nine, said in a statement.
"It has been a dream year and to be one of the eight qualifiers in singles and also compete in the doubles is something that makes me very proud.
"There have already been so many highlights this year, and I hope to finish it playing some more great tennis in front of the amazing Singapore crowd."
World number one Serena Williams, who narrowly missed out on a rare calendar Grand Slam, decided earlier this month that she would not be defending her WTA Finals title, citing the need to allow her body to heal.
Safarova joins Simona Halep, Garbine Muguruza, Maria Sharapova, Petra Kvitova, Agnieszka Radwanska, Angelique Kerber and Flavia Pennetta in the Singapore singles field.
Swiss Timea Bacsinszky and former world number one Venus Williams are first and second alternates.
(Reporting by Patrick Johnston; Editing by Peter Rutherford)
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