Yonel Brown led Kennesaw State (1-4) with 15 points.
Mississippi State led 35-31 at halftime despite Kennesaw State shooting 54.2 percent from the floor. The Owls hit eight of their first 10 shots of the game, but the Bulldogs took the lead for good on Thomas' free throw at the 8:33 mark of the first half.
Mississippi State shot 47 percent and made 8 of 23 3-point attempts.
Thomas sat out Mississippi State's first game of the season due to a one-game NCAA suspension after playing in a non-sanctioned NCAA all-star game over the summer. Thomas was 6 of 14 from the floor and 4 of 8 beyond the arc for the Bulldogs.
Mississippi State and Kennesaw State both grabbed 33 rebounds while the Bulldogs forced 26 turnovers and had just 12 turnovers.