Moussa Sow's first-half goal on a header was the difference in the game.
Instead of his usual position at left back, Bocanegra played in the middle of the backline.
Rennes will face Toulouse or Guingamp at the Stade de France in the final on May 9.
Grenoble's best chance came when Pierre Boya hit the woodwork shortly before the interval.
St. Etienne 2-0