The three-time champion also hailed her British opponent, and described her career as a "great adventure".
"I want to thank you all. One of my biggest dreams came true in 2005 winning here and every time I came back I have been inspired by the energy on this court," she said.
"I have played some of my greatest tennis here, It feels like the perfect place to retire, I just wish it was not today.
"Laura played extremely well, I fought and gave it all but I just was not good enough. It has been a great adventure, it has all been worth it, but I am looking forward to the next part of my life."
Clijsters will still compete in the women's doubles and mixed doubles in New York, but is calling time on her career after the tournament.