The former world number one, who is just six months into a comeback, fell heavily on her right elbow during her fourth-round loss to fellow Belgian Kim Clijsters and tests revealed the damage will force her to miss the last Grand Slam of the year.
"I took several medical examinations that have revealed a partial ligament fracture of the right elbow," she said on her website on Thursday.
"This injury will keep me away from the courts for a rough period of two months, with the consequence that I have withdrawn from the US Open (starting Aug. 30)," she added.
Henin said she would undergo more tests in about four weeks that would determine when she might be able to return to the courts.
The injury is a setback for the seven-time grand slam winner, who stunned the tennis world when she walked away from the game in 2008 when she was still at the top and worked as an ambassador for Unicef in central Africa and south-east Asia.
She returned to tennis earlier this year and showed that she had lost little of her touch as she made the final of the Australian Open, losing to world number one Serena Williams, but has not yet added to her collection of Grand Slam titles.South Africa fear nobody, says coach Parreira
Paes-Dlouhy in semis of UNICEF Open
Serena Williams retains her Australian Open title
Soccer boosts travel bookings for South Africa
Paes-Dlouhy in QFs of UNICEF Open