Sam Houston State (14-0) was playing in the semifinals for only the second time in their history having lost ironically to Montana (12-3) in 2004.
The Bearkats scored 21 points in the opening quarter. Quarterback Brian Bell finished Sam Houston State's first series after Montana was forced to punt to begin the game with an 11 yard touchdown run at the 10:36 mark of the opening frame.
Following a missed field goal attempt by the Grizzlies from 48 yards away, Flanders took the next play from scrimmage for the Bearkats 69 yards to paydirt at the 6:00 mark of the first quarter.
After a fumble by Montana quarterback Jordan Johnson, Bell found wide receiver Grant Merritt for a 20 yard touchdown reception to extend the Bearkats lead to 21-0 at the 1:42 mark of the opening period.
The two teams exchanged possessions to start the second quarter; Montana failing to convert a fourth-and-one play at the Bearkat 5 yard line and the Bearkats punting for the first time in the game.
Montana then finally hit the scoreboard with a 30 yard pass to Jabin Sambrano from Johnson to cut the Bearkat lead to 21-7 at the 6:27 mark of the second quarter.
Sam Houston State, however, would answer right back as Bell hit Trey Diller from 18 yards out to extend the SHSU lead to 21 points at 28-7 at the 2:15 mark of the opening half.
Following an interception by Bookie Sneed for the Bearkats, it appeared as if the SHSU may score again. Montana linebacker Caleb McSurdy, however, had other ideas. He deflected a pass from Bell and returned it back for a 61 yard touchdown to pull Montana back to within 28-14 just before the halftime break.
Bearkats kicker Craig Alaniz hit a 25 yard field goal in the third quarter that was a result of another fumble by Montana to make the score 31-14.
After that, Montana began cutting into the deficit.
Jordan Canada finished a 10 play, 61 yard drive with a three yard touchdown run to make it 31-21, and quarterback Jordan Johnson's 54 yard touchdown run drew the Grizzlies within three at 31-28 with over 11 minutes left to play in the game.
The Grizzlies were moving again to the SHSU 49 yard line on their next possession, but Johnson threw incomplete on a third-and-11 play with about six minutes left to force a Montana punt.
After that, Montana would never get the ball back.
Flanders sealed the Bearkat win with a 22 yard run on fourth and one from the Bearkats' 47 near the 2 minute mark and a couple of kneel downs ran out the rest of the clock.
The Bearkats finished on offense with 496 yards and their top-ranked rushing defense held Montana to just 103 yards on the ground.
Johnson completed 21-of-33 passes for 277 yards in the losing cause for the Grizzlies.
The biggest statistic causing the outcome was likely that Montana turned the ball over three times, where as Sam Houston State had just one.
Sam Houston State will play the winner of Saturday's semifinal between North Dakota State and Georgia Southern in the national title game on Jan. 7 in Frisco, Texas.