The fifth-seeded Slovakian dropped the initial set 2-6, but took the final two sets from Makarova 6-4, 6-2 to advance at Moscow's Olympic Stadium.
Cibulkova bested Estonia's Kaia Kanepi in the 2011 title match. She now goes on to face Bulgarian Tsvetana Pironkova, who bested American Varvara Lepchenko 6-0, 7-6 (7-3) Tuesday.
The news wasn't as good for sixth-seeded Russian Nadia Petrova, however. She was upended by Romanian Simona Halep 3-6, 7-5, 7-5 in a 3-hour-plus struggle.
Other Day 2 winners included Kazakhstan's Yaroslava Shvedova, France's Alize Cornet and Serbian qualifier Vesna Dolonc.
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