Russia's Kirilenko prevailed in what the WTA said was the longest women's singles tiebreaker at a Grand Slam tournament to knot the fourth-round match at a set apiece.
But it was the ninth seed from Australia who moved on to a quarter-final clash with second-seeded Russian Vera Zvonareva.
Zvonareva advanced with a 6-2, 6-3 victory over Sabine Lisicki, the big-serving German who had hoped to improve on her run to the Wimbledon semi-finals.
Instead Zvonareva, runner-up to Kim Clijsters here last year, needed just 77 minutes to wrap up her fourth career victory over Lisicki in as many meetings.
Stosur had already entered the record books this week when she toiled for three hours and 16 minutes to get past Nadia Petrova 7-6 (7/5), 6-7 (5/7), 7-5 in the third round -- the longest women's singles match recorded at the US Open since the tiebreak era began in 1970.
Italy's Flavia Pennetta also stayed tough in the face of adversity as she carved out a 6-4, 7-6 (8/6) victory over a fighting Peng Shuai to set up a quarter-final meeting with German Angelique Kerber -- a 6-4, 6-3 winner over Monica Niculescu in a battle of unseeded players.
Pennetta, the 26th seed, who shocked third-seeded Maria Sharapova in the third round, had to fight to the finish against Peng, who saved one match point and gave herself four set points in the tiebreaker before Pennetta was able to reach the quarter-finals for the third time in four years.
Pennetta twice came back from service breaks in the second set, but after breaking Peng for a 6-5 lead she was clearly feeling the strain of the long rallies on the steamy Louis Armstrong Stadium.
Serving for the match, she had to pause at the back of the court as she felt herself becoming ill, returning to the baseline to cheers of encouragement of the crowd -- and a time warning from the chair umpire.
The quarter-final line-up will be completed on Monday when world number one Caroline Wozniacki faces 2004 champion Svetlana Kuznetsova and three-time champion Serena Williams will tackle another former world number one, Ana Ivanovic.
