Instead, the seven-times grand slam winner Henin took the set in a tiebreak before wrapping up the win.
Henin won all four of her break points in the match while Jankovic converted only three out of nine.
The Belgian will face the unseeded Israeli Shahar Peer in Saturday's semi-final at the indoor clay tournament.
“I still need time to adjust”
Speaking after her win, Justine Henin told journalists that "I still need time to get used to clay.”
"I haven't played on this surface for two years. I grew up on this surface and my best results are on this surface but I try to be a complete player."
Wildcard Henin added: "It's only my fifth tournament back, it's normal to have ups and downs."
"I feel fresher than two years ago. I really needed the time off. Just to have the experience which I didn't have before as a person gives me a lot."