Gray suffered a right Achilles injury that will require surgery. The sophomore was the third-leading rusher in the Big 12 at 780 yards and four touchdowns on 159 carries.
Whaley's breakout senior season is finished after he suffered a left knee injury in the first quarter.
The defensive tackle recorded 25 tackles, five tackles for loss and two sacks on the year and had an interception for a touchdown in a win over Oklahoma, and a fumble recovery for a touchdown to help Texas beat Kansas.
Whaley was carted off the field early in the first quarter with the leg injury. In his place, backup defensive tackle Desmond Jackson recorded eight tackles (2.5 for loss), two sacks and recovered a fumble.
After losing quarterback David Ash earlier this season, Texas shifted to a run-heavy offense led by Gray and Brown. Gray surpassed 100 yards in wins against Kansas State and Oklahoma and rushed for 571 yards on 4.7 yards per carry in Big 12 play.
The Longhorns had already lost another key starter, top linebacker Jordan Hicks, for the season to a ruptured left Achilles. Ash has not played in a game since Sept. 21 because of the lingering effects of a concussion.