During the error-filled match, the third-seeded Serbian broke Schnyder, the 14th seed, in all of her eight service games.
Schnyder's victory came one day after she eliminated Australian Open champion Serena Williams in the quarterfinals.
"I expected a tough match, because Patty played well yesterday," Jankovic said.
In Saturday's other semi, second-seeded Svetlana Kuznetsova of Russia topped ninth-seeded Slovakian Daniela Hantuchova, 6-4, 6-2.
"I always try to expect a tough match because if the match ends up being easy it's always better," Kuznetsova said. "Daniela is playing much better than she was in the past year, but I know I'm better on clay courts definitely."
Sunday's Jankovic-Kuznetsova winner will earn $181,980 with the French Open looming in nine days.