Towson (13-2) took over on its 29 with 1:35 left in the game and went 71 yards for the winning points.
Eastern Washington (12-3) got the ball back with 12 seconds left, but Vernon Adams' first pass was intercepted.
Towson will play two-time defending champion North Dakota State (14-0) in the national title game on Jan. 4 in Frisco, Texas.
Eastern Washington was makings its third trip to the semifinals in four seasons, and won the 2010 national championship.
The Tigers have won 12 straight games on the road dating to last season, and overcame the loss of starting quarterback Peter Athens to a shoulder injury.
Towson scored the first 21 points of the game, gave up 31 straight points, and then scored the final two touchdowns for the win.
Adams threw for 394 yards and two touchdowns for Eastern Washington, which outgained the Tigers 580 yards to 483.
Frazier completed 6 of 10 passes for 98 yards, and also ran 18 times for 98 yards and the winning touchdown.
Towson marched 75 yards down the wet, slippery field on its first possession, with Athens throwing a 1-yard touchdown pass to Emmanuel Holder for a 7-0 lead
Eastern moved down the field on its first possession, but receiver Cooper Kupp fumbled on Towson's 12 and the Tigers recovered. Derrick Joseph caught passes for 50 and 16 yards for Towson, and Terrance West dove over from the 1-yard line for a 14-0 lead. It was West's FCS-record 40th touchdown of the season, 39th on the ground.
After a pair of EWU punts, Towson drove 91 yards in seven plays to take a 21-0 lead. The drive ended when on fourth down Athens threw a 38-yard touchdown pass to Brian Dowling in the end zone with 10:32 left in the first half.
Eastern Washington finally scored when Adams threw an 8-yard touchdown pass to Quincy Forte midway through the second quarter.
Towson fumbled on its next possession and Eastern Washington's Will Katoa recovered on his own 36. Starting with just two minutes left in the half, the Eagles drove to the 1, but time expired when Adams was stopped while trying to run into the end zone.
Towson amassed 309 yards of offense in the first half but Athens was not able to play in the second half because of a shoulder injury. He had thrown for 144 yards and the touchdowns. Frazier was unable to move the offense until late in the fourth quarter.
Eastern Washington opened the second half with a 10-play, 92-yard drive that ended with Forte's 7-yard touchdown run, cutting Towson's lead to 21-14.
After Towson punted, the Eagles drove to the Tigers 5, but had to settle for Kevin Miller's 22-yard field goal to cut the deficit to 21-17.
Towson went three-and-out, and the Eagles' Zach Wimberly blocked the punt, allowing Eastern Washington to take over on the Tigers' 23. Mario Brown ran the ball twice, the second a 5-yard touchdown run as Eastern Washington took the lead at 24-21 with 1:36 left in the third.
Towson punted again and the Eagles went 82 yards, with Adams hitting Cory Mitchell on a 12-yard touchdown pass for a 31-21 lead. It was the 55th touchdown pass of the season for Adams.
West ran 3 yards for a touchdown on Towson's next possession, completing a 75-yard drive that featured 13 running plays. It was the first second-half touchdown Eastern Washington has allowed in three playoff games this season and cut the Eagles' lead to 31-28 with 5:09 left.
Eastern Washington burned clock time on its ensuing drive, and turned the ball over on downs with 1:35 left.
Towson, taking over on its own 29, moved down to the 1 yard line with 25 seconds left. West was stopped on a run. Then Frazier scored on a quarterback sneak with 17 seconds left for the win.