The fifth seed Wozniacki dropped the first set against the Russian 6-4 but won the next 6-0 despite having a long rules debate with the umpire and a line judge after being charged with a foot fault.
She took the final set 6-3 to set up a semi-final meeting with American surprise package Jamie Hampton.
Hampton, who had to qualify for the event, continued her superb run in East Sussex with a 3-6 7-6(1) 6-4 victory over Lucie Safarova.
Second seed Li Na suffered a surprise defeat though as she lost 7-6(4) 6-3 to Heather Watson's conqueror Elena Vesnina.
Vesnina will play Yanina Wickmayer in the last four after the Belgian upset sixth seed Maria Kirilenko 6-2 1-6 7-5.
WTA Eastbourne quarter-final results
Yanina Wickmayer (Belgium) beat 6-Maria Kirilenko (Russia) 6-2 1-6 7-5
5-Caroline Wozniacki (Denmark) beat Ekaterina Makarova (Russia) 4-6 6-0 6-3
Elena Vesnina (Russia) beat 2-Li Na (China) 7-6(4) 6-3
Jamie Hampton (U.S.) beat Lucie Safarova (Czech Republic) 3-6 7-6(1) 6-4
WTA 's-Hertogenbosch quarter-final results
4-Kirsten Flipkens (Belgium) beat 7-Urszula Radwanska (Poland) 6-4 6-4
Garbine Muguruza Blanco (Spain) beat 2-Dominika Cibulkova (Slovakia) 6-4 6-4
Simona Halep (Romania) beat Lesia Tsurenko (Ukraine) 6-3 6-1
3-Carla Suarez Navarro (Spain) beat Tsvetana Pironkova (Bulgaria) 2-6 6-4 6-4
- Sports & Recreation
- Elena Vesnina
- Lucie Safarova