Kelly said that Jones has a third-degree MCL injury in his right knee and will undergo surgery next week.
Jones, a redshirt junior, was making his return from a Lisfranc injury in his foot suffered in a Nov. 22 loss to Louisville, which cost him the final two games of last season along with this spring season.
The 6-foot-5, 315-pound Jones figured to play a major role in the middle of the Fighting Irish's defensive line. He had started all 11 games last season until the foot injury, tallying 40 total tackles, including 7.5 tackles for loss and 1.5 sacks, along with seven quarterback hurries, one forced fumble and two blocked kicks.
The 11th-ranked Fighting Irish open at home Sept. 5 against Texas.