The 21-year-old produced a flawless display to take the first set without dropping a game.
She then looked to be on her way to victory when she broke Jankovic early in the second but the Serbian recorded a break of her own to pull the set back to 4-3.
With Wozniacki serving for the match, Jankovic broke again to level the second set at 5-5.
However the Dane showed her class by winning the next two games to take the set 7-5 and the match in straight sets.
Wozniacki will meet Belgian Kim Clijsters for a place in the last four in the standout tie of the quarter final stage.