The Serb pulled back from 4-1 down in the first set and had a set point on serve at 6-5 before losing the tiebreak. Jankovic then, twice, recovered breaks in the second set but Martinez Sanchez clinched the biggest title of her career after breaking for the third time.
Former world number one Jankovic beat Serena and Venus Williams earlier this week but fell short in her bid for a third Italian Open title.
Sanchez signalled her intent from the start, getting Jankovic scrambling to the net to recover drop shots. The Serb crouched down on her knees for a few seconds after going down 4-1.
Martinez Sanchez let Jankovic back in the match with some unforced errors and wasted a set point at 5-4 but still managed to take the set with a smash at the net.
She kept mixing it up and proved her groundstrokes were not shabby either, rifling a splendid backhand winner to break for the third time in the second set to go 6-5 up.
Martinez Sanchez then clinched victory by nailing her second match point with a serve and volley winner.
Jankovic, the 2007 and 2008 champion, will climb to fourth in next week's rankings after reaching the final.
