The Heisman Trophy-winner played about a quarter more than he did last week when he sat out the first half serving a suspension for what the school called an "inadvertent" violation of NCAA rules involving signing autographs.
Texas A&M's suspension-depleted defense was burned for several big plays by the Bearkats (1-1), the FCS runner-up the last two seasons, in the final tuneup before next week's rematch with top-ranked Alabama.
Sam Houston's Timothy Flanders had 170 yards rushing with two scores and added a TD reception.
Texas A&M's Mike Evans had a career-high 155 yards receiving, Tra Carson ran for 51 with two touchdowns and Ben Malena had 68 yards rushing and a score.
Freshman Kenny Hill added 74 yards passing to give A&M a school-record 500 yards passing and the Aggies (2-0) had 38 first downs to tie the school mark.
Manziel threw an interception in the first quarter, but looked sharp otherwise, distributing the ball well as he completed passes to nine different players in the first half.
The Bearkats cut the lead to nine points when Flanders gashed through the line for a 68-yard touchdown run on the second play of the third quarter.
Carson scored on a 1-yard run before Manziel threw a 10-yard pass to Brandon Williams to extend the lead to 44-21.
Another big play - this one a 75-yard reception by Torrance Williams - got Sam Houston State within 44-28.
Manziel finished his day with a 6-yard touchdown run with about five minutes left in the third quarter. He seemed to get annoyed at a defender who knocked the ball out of his hands after the score. He jawed for a few seconds, but he handled himself much better than he did a week ago when he drew a flag for taunting the Rice defense and was benched late in the fourth quarter.
Cornerback De'Vante Harris, linebacker Steven Jenkins and defensive end Gavin Stansbury missed the game serving the last of two game suspensions for violating team rules. Cornerback Deshazor Everett was suspended for the first half for a targeting penalty last week.
Everett had an interception in the third quarter.
The game was tied at 7 before the Aggies scored three straight touchdowns to push the lead to 27-7. Manziel found Sabian Holmes on a 27-yard pass for the first score before Malena's 1-yard run put A&M up 20-7 early in the second quarter. There was a bad hold on the extra point after Malena's score and Taylor Bertolet's kick failed.
Manziel ran for 6 yards and lowered his head and bulled over cornerback Shelby Davis near the goal line for what was first ruled a touchdown on the play before Malena's score. A review determined that Manziel stepped out of bounds at the 1.
Manziel floated a perfect pass into the corner of the end zone that Ja'Quay Williams stretched out to grab for a 20-yard touchdown about 4 1/2 minutes before halftime.
Flanders added a touchdown when the Aggies bit on a fake and Brian Bell found him wide open for a 33-yard score which cut the lead to 27-14 with about two minutes left in the first half.
Bertolet's field goal as time expired in the second quarter made it 30-14.
Sam Houston State tied at 7-all with about eight minutes left in the first quarter when Flanders scored on an 11-yard run. It capped an 81-yard drive where the Bearkats did it all on the ground. Flanders had a run of 20 yards on the play before the touchdown.
Linebacker Eric Fieilo intercepted Manziel just outside of the end zone on A&M's next drive, but the Bearkats couldn't take advantage of the error and soon had to punt