By reaching the semi-finals, the 21-year-old Henin-Hardenne leap-frogged compatriot Kim Clijsters, who had held the top spot almost continuously since August, to became the first Belgian to secure the year-end ranking.
She is only the eighth player since the WTA introduced the rankings in 1975 to hold the year-end top spot.
"It's just amazing. The season has been great," Henin-Hardenne, who won the French and U.S. Open titles said.
"It's just unbelievable how things have changed in the last few months. Sometimes I wake up and say I can't believe what's happened.
"But I know the reasons. I'm working harder and feeling good personally. I'm totally happy right now."
Clijsters also reached the semi-finals winning a tough battle over France's Amelie Mauresmo 3-6, 6-4, 6-4 while Russian Anastasia Myskina stayed alive in the Black Group with a 6-4, 6-3 victory over Japanese Ai Sugiyama, who is now out of the competition.
Myskina and Capriati will play off for a place in the semi-finals on Saturday.
Clijsters was unable to hang on to the top ranking after Henin-Hardenne won San Diego, Toronto, the U.S. Open and Zurich.
Saddled with a strained right hip flexor, Capriati was simply no match for Henin, who recovered quickly from her two and-a-half-hour victory over Anastasia Myskina on Thursday night and ran circles around the American.
Unlike their spectacular three-set battle at the U.S. Open two months ago, Capriati could not hang with the speedy Henin in extended rallies, nor could she find power or depth on her groundstrokes.
"I don't think I could move to my fullest capability," said Capriati, who added that she would not have played if it had been a smaller tournament.
"I just didn't feel like I could go all out. That with her playing well is a tough combination."
After Henin cracked a service winner to take the first set, Capriati took an injury time out to have her thigh wraps removed, which she said were burning her skin.
She played a little better at the start of the second set, but Henin broke her to 2-1 with a forehand crosscourt winner and never looked back, winning the contest when Capriati erred on a backhand volley.
