Jankovic wasted three break points at 1-1 in the last set before Mauresmo seized her chance in the next game, hitting a forehand winner across court for a 3-1 lead.
Mauresmo converted her third match point on a backhand from Jankovic that went long.
In the opening set, Mauresmo took Jankovic's serve for a 3-1 lead and saved a break point at 4-2 with a forehand that caught the tape.
Jankovic then handed Mauresmo the first set with a forehand that went long.
But the third-ranked Serb fought back, winning the next six games to clinch the second set on a forehand error from Mauresmo.
Williams said she hurt her knee during Friday's match against Emilie Loit and was in too much pain to attempt to play leaving the fourth-ranked Dementieva to reach the final for the first time in eight appearances at the tournament.
"It's just unfortunate we couldn't play,'' Dementieva said. "I feel sorry for her. This is not the way you want to be in the final.''
Williams, who won the Open GDF Suez in 1999 and 2003, said her injury may be the result of playing too much.
"My left knee always hurts, but this time it's my right knee,'' the American said. "When I woke up this morning, it wasn't feeling good. I wasn't moving well at all in practice. It was just really no chance.
"I've been playing a lot of tennis. Maybe it's just a sign that I need to take a day off or two and get ready for the next event,'' said the Australian Open champion, who is set to play in the Dubai Championships next week.
"I'm gonna make the effort to play and be there,'' Williams said. "I just think I'll be OK. I just have to make sure it stays strong.''
Serena withdraws; Mauresmo, Dementieva in final
Ronaldo Talks Of Recovery A Year After His Horrific Knee Injury
Serena withdraws; Mauresmo, Dementieva in final
