The loss came on Court 2, which is called "The Graveyard of Champions," and means that the Wimbledon women's final will be missing at least one of the Williams sisters for the first time since 1999.
The only player other than Venus or her sister, Serena, to win the event the previous six years was Maria Sharapova in 2004.
Venus hit 50 winners to 27 for Jankovic, but was undone by 12 double faults and 54 unforced errors.
"I had some opportunities, but unfortunately she played some good tennis," Williams told the BBC. "I would have liked to have played better. I didn't get to the net enough."