The Serb came flying out of the blocks and had the Belgian on the back-foot for a set and a half, before her inexperience began to tell and Henin-Hardenne fought back to book a place in her fourth Grand Slam final of the year.
The 2003 champion served 12 double faults in the first two sets and becomes only the second woman to reach all four grand slam finals in the year after Martina Hingis in 1997.
"I feel very lucky to be in the final," Henin-Hardenne said. "I was a bit nervous at the beginning of the match. She put a lot of pressure on me and I wasn't in a good rhythm.
U.S. Open
Navratilova hits 50
18/10/2006 AT 13:47
"But I kept fighting and finally I was able to come back. This was maybe the kind of match I would have lost a year or two ago."
In her first grand slam semi-final, the 21-year-old Jankovic played aggressively and took advantage of her subdued Belgian opponent to lead by a set and 4-2.
But - after missing a point for 5-2 - the nerves seemed to get to the Serbian and Henin-Hardenne won 10 straight games as she eased through to a clash with third-seeded Russian Maria Sharapova.
At 4-2 in the second set, Jankovic seemed poised to complete a major upset but after a dispute with the umpire she lost her focus.
Jankovic said: "My concentration went down because of the umpire. He didn't know if the ball was in or not.
"Then I make the double fault on the game point. I think that was a huge point for me. I could have been 5-2 up and it would have been a very different story."
During the second set Henin-Hardenne looked to be struggling but after taking the second set recovered and looked the fitter of the two players by the end of the match.
"I couldn't serve a lot during practice," she said of a back injury that has been niggling for the past few days.
"But I think every athlete has to deal with a little bit of pain at the end of a grand slam."
Despite her defeat, Jankovic was delighted with her achievements, having never gone beyond the fourth round of a grand slam event before.
"I'm disappointed that I lost in the semi-final, but I am young. I will learn from my mistakes and this is a new experience for me," she said.
"I couldn't ask for more, I was in the semi-finals of this tournament and I am really grateful."
U.S. Open
Federer will end year No. 1
11/09/2006 AT 21:55
U.S. Open
Euro spout - Who is the greatest?
11/09/2006 AT 17:08