before falling to the world number one Dinara Safina of Russia and had lead Jankovic head to head 6-0.
At Cincinnati, Clijsters in the third round upset the French Open champion Svetlana Kuznetsova of Russia in the third round as well as the Stanford champion Marion Bartoli of France in the opening round.
This week in her prior round, the Belgian knocked off the Miami champion and ninth seeded Victoria Azarenka of Belarus in the second round.
Clijsters began Thursday's contest strongly as she jumped out to a 5-0 first set lead before Jankovic held serve to reach 5-1. But the Serb was only able to win 20% of her service points and 14 points overall as she would drop the set 6-1 in only 26 minutes.
Flashing some of her trademark smiles and showcasing a growing fighting spirit, Jankovic saved two breakpoints in her opening service game of the second set before delivering an ace on game point to lead 1-0.
Jankovic broke serve to lead 2-0 but suffered a temporary setback as Clijsters pulled even at 2 all.
The Serb then posted a 5-2 lead before closing out the set 6-3 after one hour and one minutes of play.
The pair's prior last three encounters had been decided in a third set and Clijsters quickly went ahead in Thursday's final set 40-0 before holding serve to lead 1-0.
And for all of her fight throughout set two, Jankovic who'd last week taken the Cincinnati title, found herself in a struggle in the decisive third set as she held serve to reach 3 all.
Clijsters survived a five deuce game to break serve for a 5-3 lead but then dropped the last four games of the match as Jankovic would prove to be the more steady of the two players finally.
But in a validation of the Belgian's comeback success, the United States Tennis Association Thursday awarded Clijsters a US Open main draw singles wild card. In her last US Open appearance, Clijsters took the 2005 singles title defeating Mary Pierce of France in the final for her lone singles grand slam win.
When the US Open begins August 31, fireworks could fly straight away as Clijsters will not be ranked high enough to be seeded if she is ranked at all. This means Clijsters could meet a top player such as the second ranked Serena Williams of the USA or Safina in the first round of play.
Williams took the 2008 US Open title beating Jankovic in the final.