The Heisman Trophy winner started despite an apparent shoulder injury, and threw for 305 yards with four touchdowns and an interception.
He was more conservative running the football, picking up just 11 yards on four carries.
Matt Joeckel replaced Manziel in the third quarter with the Aggies comfortably ahead 42-17.
Before the game, Manziel participated fully in warm-ups with the team and took the first team snaps in 7-on-7 drills.
Manziel was limited in practice throughout the week but has thrown as much he has been able to, according to sources. Manziel, who suffered the injury to his throwing shoulder in Texas A&M's 45-41 loss to Auburn last week, was called "hopeful" to play by coach Kevin Sumlin earlier this week.
Manziel injured his right shoulder when he was tackled by two Auburn defenders at the end of an 8-yard run with 14:36 remaining in the fourth quarter against Auburn. Manziel grabbed his right shoulder before getting up then fell to the turf as he was walking back to the sideline and was attended to by the Aggies' training staff.
When testing his throwing arm by trying to throw a football on the sideline, Manziel could be seen wincing from the pain. He received treatment from the A&M training staff and returned to the game with 9:06 to go.
Upon his return he completed 9-of-10 passes for 102 yards and ran for a touchdown. He finished the day 28-of-38 passing for 454 yards and four touchdowns and 18 carries for 48 yards and a touchdown.
Throughout the week, Sumlin offered little more than simply calling Manziel "hopeful" for the game and did not disclose the details of the injury or Manziel's rehabilitation.
Manziel has thrown for 2,289 yards and 18 touchdowns with seven interceptions while completing 73.3 percent of his passes this season. He has rushed for 486 yards and six touchdowns.
Joeckel and true freshman Kenny Hill are the backups, with Joeckel likely to be first off the bench should Manziel need relief at some point today. Joeckel started the season opener against Rice when Manziel served a two-quarter suspension on Aug. 31.