Four-times champion Wozniacki's winning streak at Yale came to an abrupt end when she was forced to retire midway through her semi-final with Kirilenko, the Dane citing a knee injury.
The former world number one had just dropped the first set 7-5 when she called the trainer and threw in the towel.
"I could feel it from the start," said Wozniacki, who picked up the knock in her quarter-final against Dominika Cibulkova.
"But, you know, it just started to get a bit worse. I decided to stop because if you don't feel a hundred percent, you can't compete at a hundred per cent.
"It's better to let it rest. I wasn't going to win this match anyways if I'm not on a hundred percent fit level."
Wozniacki had previously won each of the 20 matches she had played at the pre-US Open warm-up tournament.
Seventh-seeded Kirilenko will face Kvitova for the title after the world number five eased past Italy's Errani 6-1 6-3.
The powerful Czech blitzed the fourth seed in an opening set that lasted just 24 minutes before breaking early in the second and never looking back.
"The run that I have here in North America, it's the first one," Kvitova said. "I didn't have a great result before, so I'm really glad for it."
The US Open starts in New York on Monday.