The Serbian, pushed hard in her previous two matches, again became embroiled in a war of attrition but her superior fitness and strength proved key as she rallied for victory.
“I had to really play a lot more aggressive because it's quite windy and she was a lot more solid than I was in the first set,” Jankovic said.
The 18-year-old Wozniacki, seeded 21st, out-manoeuvred Jankovic in the first set but as the match wore on the Serbian began to win the majority of the longer rallies. After levelling the match, she broke in the fourth game of the third set and then eased through the next three games to clinch victory.
Japanese outsider Kei Nishikori stole the spotlight on another day of shocks at the US Open while Venus and Serena Williams rolled towards a quarterfinal showdown at Flushing Meadows.
Fourth seed David Ferrer was left a punched out wreck as he went down 6-4 6-4 3-6 2-6 7-5 following an inspired performance by Nishikori.
The 18-year-old made his ranking of 126 look like a mathematical error during the 3-1/2 hour tussle and he kept his nerve to become the first Japanese man since 1937 to reach the last 16 in New York.
He will next face rising Argentine Juan Martin Del Potro, who tamed French 16th seed Gilles Simon 6-4 6-7 6-1 3-6 6-3. Rafael Nadal can expect an easy ride into the semifinals after his draw opened up following the defeats of seventh seed David Nalbandian, ninth seed James Blake and 14th seed Ivo Karlovic.
Argentina's Nalbandian was ousted by 32nd seeded Frenchman Gael Monfils 6-3 6-4 6-2 and hard-serving Karlovic was beaten 7-6 7-6 6-2 by American Sam Querrey. Mardy Fish completed a bad night for the seeds when he trampled over fellow American Blake 6-3 6-3 7-6.
Paes-Dlouhy through
India’s Leander Paes and his Czech partner Lukas Dlouhy entered the pre-quarterfinals with an easy 6-3, 6-3 win over Rik De Vost of South Africa and Ashley Fisher of Austria.
Earlier, Andy Murray, the British sixth seed, also looked to be on his way out when he was two points from defeat before he found his range to pull off a 6-7 4-6 7-6 6-1 6-3 win over Austrian Juergen Melzer.
World number one and Wimbledon champion Nadal, who will not face a top 30 player until at least the semifinals, blasted into the fourth round by grinding down Serbian Viktor Troicki 6-4 6-3 6-0.
While most of the men found it tough going on day six of the season's final grand slam, Venus and Serena faced no such problems.
Venus overwhelmed Ukrainian Alona Bondarenko 6-2 6-1, while younger sister Serena blew past Japan's Ai Sugiyama with an identical scoreline. "I'm definitely at my best now," seventh seeded Venus boasted after her 56-minute rout under sunny skies at the National Tennis Center. The 28-year-old, who will next face Polish ninth seed Agnieszka Radwanska, said she has added a little spice to her game since arriving at Flushing Meadows a decade ago. Dinara Safina, tipped by many as a potential champion here, almost became another big-name casualty before scrapping to a 3-6 7-5 6-2 win over Swiss teenager Timea Bacsinszky.
Former world number one Amelie Mauresmo reached the fourth round of a Grand Slam for the first time in over a year when she won 6-4 6-4 against Julie Coin.
Bhupathi-Stosur out
Mahesh Bhupathi and his Australian partner Samantha Stosur crashed out of their US Open mixed doubles event. Swede Robert Lindstedt and his Australian team-mate Rennae Stubbs defeated Bhupati and Stosur 2-6, 6-3, 12-10.
US Open Results
Men (III round): Mardy Fish (US) bt 9-James Blake (US) 6-3, 6-3, 7-6(4); Kei Nishikori (Jap) bt 4-David Ferrer (ESP) 6-4, 6-4, 3-6, 2-6, 7-5; 17-Juan Martin Del Potro (Arg) bt 16-Gilles Simon (Fra) 6-4, 6-7(4), 6-1, 3-6, 6-3; 32-Gael Monfils (Fra) bt 7-David Nalbandian (Arg) 6-3, 6-4, 6-2; 6-Andy Murray (Bri) bt Juergen Melzer (Aus) 6-7(5), 4-6, 7-6(5), 6-1, 6-3; 10-Stanislas Wawrinka (Sui) bt Flavio Cipolla (Ita) 5-7, 6-7(4), 6-4, 6-0, 6-4; 1-Rafael Nadal (ESP) bt Viktor Troicki (Ser) 6-4, 6-3, 6-0; Sam Querrey (US) bt 14-Ivo Karlovic (Cro) 7-6(5), 7-6(5), 6-2. 5-Nikolay Davydenko (Rus) bt 26-Dmitry Tursunov (Rus) 6-2, 7-6(3), 6-3.
Women (III round): Severine Bremond (Fra) bt Tathiana Garbin (Ita) 7-5, 3-6, 6-4; 6-Dinara Safina (Rus) bt Timea Bacsinszky (Sui) 3-6, 7-5, 6-2; Anna-Lena Groenefeld (Ger) bt 17-Alize Cornet (Fra) 6-4, 7-5; 16-Flavia Pennetta (Ita) bt 19-Nadia Petrova (Rus) 4-6, 6-4, 6-3; 4-Serena Williams (US) bt 30-Ai Sugiyama (Japan) 6-2, 6-1; 32-Amelie Mauresmo (Fra) bt Julie Coin (Fra) 6-4, 6-4; 7-Venus Williams (US) bt 27-Alona Bondarenko (Ukr) 6-2, 6-1; 9-Agnieszka Radwanska (Pol) bt 18-Dominika Cibulkova (Slo) 6-0, 6-3, 2-Jelena Jankovic (Serb) bt Caroline Wozniacki (Den) 3-6, 6-2, 6-1.