With the performance, Flanders became the all-time leading rusher for the Bearkats. The Southland Conference "Player of the Year" in 2011 has now rushed for 2,709 yards, breaking the record of 2,688 yards Charles Harris set in 1991-94.
Flanders' tallies also upped his school record for rushing touchdowns to 37.
Backup Keshawn Hill also scored twice on runs of 11 and 27 yards. Chance Nelson added an 11-yard score on a pass from Brian Bell and Terrance Robinson returned a punt 60 yards for a Bearkat touchdown.
Trent Rios caught an 18-yard pass from Zach Rhodes to complete a 36 yard drive after a first quarter interception for Incarnate Word's only touchdown. The Cardinals held a brief 7-6 lead with 5:13 to play in the first quarter.
Sam Houston held a 20-7 lead at halftime but rolled off 34 points in the second period.
Sam Houston State entered the game ranked No. 1 in the Sports Network FCS national rankings. The Bearkats are defending Southland Conference champions and reached last year's NCAA Division I national finals after a 14-1 record.