A team source said the fear is a torn ACL, but Chryst is expected to undergo an MRI on Saturday to confirm any diagnosis. News of the injury was first reported by Fox Sports and confirmed by ESPN.
Chryst immediately grabbed and favored the knee after being tackled on a scramble to the right side. Trainers helped him limp to an injury tent on Stanford's sideline, and an injury cart took Chryst to the locker room.
Chryst, wearing sweats, returned to the Stanford sideline, moving with crutches and with ice applied to his knee.
Chryst replaced Burns in late October, starting the final five games of Stanford's regular season -- all wins. Chryst entered the Sun Bowl having thrown for 837 yards and rushed for 145 this season, while accounting for 11 touchdowns and two interceptions.
Chryst completed three passes before his injury in the Sun Bowl, including a 49-yard touchdown to Bryce Love.
The Cardinal also played without star running back Christian McCaffrey, who opted to skip the Sun Bowl to focus on his preparations for the 2017 NFL draft.
ESPN's Kyle Bonagura contributed to this report.