Mauresmo, who went into the event as the top-ranked woman in the world, got the better of two-times winner Clijsters in a titanic struggle at the Madrid Arena.
There was nothing to separate the two players until Mauresmo got the crucial break in the deciding set to go 5-3 up after a failed line-call challenge from Clijsters, and she then served out for victory to give her a chance to defend her title.
Mauresmo won the last four games of the final set as she recovered from a Clijsters break to love which had given the Belgian a 3-2 lead for what was her first lead of the entire match.
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Mauresmo's response to that set back was stunning as she broke also managed to break Clijsters to love, before winning the next three games to take the match.
It was also a stunning comeback for the Frenchwoman who had lost her opening match of the week in straight sets against Nadia Petrova.
"I'm very proud with way I have hung in there all week," she said.
"All week my game has just got better and better and tonight I am just going to relax, have a massage and just get ready for the match tomorrow"
Mauresmo will now play Justine Henin-Hardenne in the final, after the pint-sized Belgian produced a stunning performance to beat Maria Sharapova 6-2 7-6.
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