The Danish world number 11 lost the opening set and had to come through a tie-break in the second before sealing victory over the Slovakian world number 32.
“It was a great match and I am really happy for my victory. Tomorrow I will enjoy my day off,” Wozniacki said.
Wozniacki has now won all three of her matches and tops Group Serdika ahead of Italy's fourth seed Roberta Vinci, who has two wins in three matches after she beat Taiwanese fifth seed Hsieh Su-Wei 6-1 6-2 in a one-sided match.
Second seed Nadia Petrova beat fellow Russian and third seed Maria Kirilenko 3-6 7-6(4) 6-3 in the only Group Sredets match to be played on Thursday.
The match lasted nearly three hours and the effort proved too much for Kirilenko, who afterwards pulled out of the tournament citing an upper respiratory illness.
Her withdrawal means Petrova, top of the group with two wins from two, automatically qualifies for the semi-finals along with Bulgaria’s Tsvetana Pironkova. Those two will meet on Friday to determine who qualifies second from the group.
Kirilenko said: "I'm very sorry that I cannot continue to play my matches here. It was such an honour to receive the wildcard ... unfortunately with this illness I can't finish the tournament as I'd have wished."
4-Roberta Vinci (Italy) beat 5-Hsieh Su-Wei (Taiwan) 6-1 6-2
1-Caroline Wozniacki (Denmark) beat 7-Daniela Hantuchova (Slovakia) 3-6 7-6(4) 6-4
2-Nadia Petrova (Russia) beat 3-Maria Kirilenko (Russia) 3-6 7-6(4) 6-3