Ballard ran 60 yards for a score to forge a 7-7 tie late in the first quarter and then sprinted 72 yards early in the fourth to give the Bulldogs a nine-point lead.
Mississippi State overcame four turnovers to finish its season at 7-6. Wake Forest wound up with a 6-7 record, losing six of its last seven games.
The Bulldogs went in front for good in the second period on a 31-yard scoring pass from Chris Relf to Arceto Clark and boosted their advantage to 16-7 at halftime on Derek DePasquale's 33-yard field goal.
Wake Forest, playing in a bowl game for the first time in three seasons, rallied to within two points on Tommy Bohanon's 1-yard run in the third period. Ballard, however, put Mississippi State in control with his second long touchdown run.
The Demon Deacons had the ball three more times after Ballard's second score. They ran out of downs in Mississippi State's end of the field, then got a field goal of 46 yards from Jimmy Newman to account for the final score.
After forcing a Mississippi State punt with 2:15 remaining, Wake Forest was unable to pick up a first down.
Ballard's 182 yards came on 13 carries. Relf completed 12-of-19 passes for 129 yards and was intercepted twice.
Wake Forest's Tanner Price was 24-of-46 for 215 yards without a touchdown or interception.
Mississippi State was the first of nine Southeastern Conference schools that will see bowl action this season. The Atlantic Coast Conference fell to 2-2, with four bowl appearances remaining.