Ward, the nation's only player to run and throw for 1,000 yards this season, threw for 238 yards and ran for 67 yards as No. 14 Houston (13-1) scored the most points allowed by Florida State this season.
The No. 9 Seminoles (10-3), who trailed 21-3 at halftime, tried to rally with two fourth-quarter touchdown passes by Sean Maguire. It wasn't enough to overcome five turnovers.
Maguire, who was carted off the field with a lower left leg injury late in the first quarter, returned but threw four interceptions. Houston safety Trevon Stewart and cornerback William Jackson III each had two interceptions.
Florida State star running back Dalvin Cook was held to 33 yards with a touchdown and a lost fumble.
Florida State committed only 10 turnovers in the regular season.
Ward, the junior who started at wide receiver early last season before becoming a full-time quarterback, had touchdown runs of 7 and 6 yards. He left the game briefly after taking a hit in the third quarter, and was shaken up again with about 4 minutes remaining. He returned to take the final snaps of the game, raising his arm in celebration before laying on his back, wallowing in the confetti which fell from the Georgia Dome roof.
Houston backup quarterback Kyle Postma's 29-yard run set up Ryan Jackson's game-clinching 2-yard touchdown run with about 2 minutes left.
Ward completed 25 of 41 passes with one touchdown and one interception.
Houston's only loss this season, to Connecticut, came when Ward was out with an injury. He kept the Florida State defense off-balance by leading the Cougars' fast-tempo, no-huddle attack.
Maguire's 65-yard scoring pass to Travis Rudolph cut Houston's lead to 24-17 early in the fourth quarter. Ward answered with a 17-yard touchdown pass to Chance Allen, who was left uncovered as Florida State sent a defensive back on a blitz. Maguire added a scoring pass to Jesus Wilson later in the final quarter.
Maguire was hurt in the first quarter when hit by Houston linebacker Matthew Adams. Maguire couldn't put pressure on his left leg as he was supported by trainers before leaving the field on a cart.
When Maguire was out, backup J.J. Cosentino completed only 1 of 4 passes for 5 yards. Maguire returned midway through the second quarter with a wrap around his left ankle and foot.
The Seminoles were without quarterback Everett Golson, the Notre Dame transfer who began the season as the starter but was away from the team for the bowl game for personal reasons.
The Seminoles, held to a field goal on four first downs in the first half, finally reached the end zone on their first drive of the second half. Maguire kept the drive alive with two third-down completions to Kermit Whitfield, and his 26-yard pass to Rudolph set up Cook's 1-yard scoring run.
On Houston's next possession, Florida State's Derwin James sacked Ward for a loss of 6 yards on a fourth-and-2 play, stopping the Cougars at the Seminoles 38.
The momentum turned back to the Cougars two plays later, when Maguire's pass was intercepted by Stewart. Later in the third quarter, Stewart added another interception when Maguire tried a deep pass for Whitfield between two defenders.
Maguire's last interception came with 25 seconds remaining. He completed 22 of 44 passes for 392 yards with two touchdowns and four interceptions.