The No.34-ranked Czech defeated four-time grand slam champion Sabalenka 6-4 6-3 in just 95 minutes on Sunday, leaving the tournament without its two top seeds in the first week.
Newly-crowned world No.1 Elena Rybakina was ousted from the tournament on Saturday and will now be joined by Sabalenka in exiting WTA 1000 event in Beijing prematurely.
The Belarusian has not lifted a trophy since completing the "Sunshine Double" with victories in Indian Wells and Miami earlier this year.
Sabalenka, who was denied a three-peat at the US Open last month by Rybakina to ensure she would finish the season without a slam win for the first time since 2022, squandered five break points in the first set as her historic struggles in the Chinese capital continued. The 28-year-old Belorussian has never progressed past the quarter-finals at the event.
"First of all, I focused on myself, to be calm," Bartunkova said.
"And Aryna, she's great, she's a legend, she's a grand slam champion. So, yeah, I'm really happy that I won the match ... I'm not a girl who celebrates too much."
Bartunkova will next play 24-year-old Sinja Kraus of Austria, who earlier defeated Dayana Yastremska 6-1 6-4.
There were also victories for fourth seeded American Mira Andreeva, 6-4 6-1 over Uzbekistan's Polina Kudermetova, and Ekaterina Alexandrova, a 3-6 6-4 6-3 winner against 11th seed Diana Shnaider.
The last remaining Australian, Taylah Preston, was later swept aside in straight sets by Daria Snigur.
The Ukrainian won 6-1 6-0 in just 47 minutes, breaking the 20-year-old twice in the first set en route to opening up a 5-0 lead.
It was more one way traffic in the second, with the West Aussie dropping all three of her service games as the world No.46 set up a clash with Andreeva.
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