Flanders rushed 21 times for 102 yards. The final drive took 5:32 off the clock. Stony Brook threw four incomplete passes to end the game.
Quarterback Brian Bell completed 11 of 20 passes for 161 yards including an 80-yard touchdown pass to Trey Diller that game the Bearkats a 27-20 lead with 8:45 to play.
Brock Jackolski rushed 14 times for 86 yards including a two-yard touchdown that tied the contest 27-27 with 6:37 to play.
Stony Brook ended the season 9-4. Sam Houston, the only unbeaten team in NCAA Division I FCS this season, advances to the quarterfinals to face Montana State.
A stingy Seawolve defense limited Sam Houston to its third lowest offensive output of the season as the Bearkats rushed for 182 yards and passed for 161 for a total of 343 yards in 63 plays.
Craig Alaniz put SHSU on the scoreboard first with a 28-yard field goal with 4:17 to play in the first quarter.
Quarterback Kyle Essington completed 9-of-29 pases for 226 yards and two touchdowns, the first a 37-yard pass to Matt Brevi that put Stony Brook up 7-3 with 8:52 to go in the second quarter.
After a 32-yard field goal by Wesley Skiffington made the score 10-3, the Seawolves went into intermission with a touchdown lead, the first time this season the Bearkats have trailed at the half.
Richard Sincere scored on a five-yard pass from Bell and Bell ran five yards for a TD to put the Kats back in front 17-10 going into the fourth quarter.
The Bearkats and Seawolves traded field goals before Essington tied the game 20-20 with a three-yard pass to Kevin Norrell.
The victory extended Sam Houston's school record winning streak to 14 games. The Bearkats now are 3-0 in NCAA Division I Football Playoff games in Bowers Stadium and will be making their third playoff quarterfinal appearance next week against Montana State.
Complete details including day and kickoff time for the Montana State quarterfinal game will be announced Sunday.
Advance tickets may be ordered tonight on www.gobearkats.com . The Sam Houston ticket office in Bowers Stadium will open sales Monday at 8 a.m.