Jones started Notre Dame's opener, a 33-3 loss at home to Georgia Tech. He was pulled as starter last Saturday against Penn State in favor of freshman Jimmy Clausen.
Jones' status at Notre Dame is now in doubt.
Against Georgia Tech, Jones was 1-of-3 passing for 4 yards and ran the ball 12 times for 28 yards. Four of the six drives he led ended in three-and-outs, and he fumbled the ball away on the other two possessions.
"At 2:30 today, while boarding the bus to Michigan, I was notified that Demetrius Jones had decided not to make the trip," Weis said in a statement. "I have not spoken to Demetrius and can only say that he missed the team bus. Any additional comment would be without all the facts."
ESPN television reporter Joe Schad contributed to this report.