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Konner Tucker was the only Bearkat in double figures with 11 points. Jonathan King, Antonio Bostic and Darius Gardner all scored 13 points for SFA.
Sam Houston ends the season 13-19 while the Lumberjacks advance to the Southland semifinals Thursday to face either Lamar or Northwestern State. SFA, the number two seed, stands 20-11 for the year.
"Give credit to Stephen F. Austin. They out-played us today," Sam Houston head coach Jason Hooten said. "Still, I'm really proud of the way our team fought through lots of adversity to fight and claw their way into the tournament this year. That says a lot about the type of young men they are."
In a first half in which the lead changed hands 11 times, neither team led by more than three points until late in the period.
Demarcus Gatlin hit a lay-up with 4:31 that gave the Bearkats their last lead of the first half, 20-19. From that point, Stephen F. Austin finished the half with a 10-2 run to go into the locker room ahead 29-22.
SFA ran the lead up to 11 points, 33-22, in the opening moments of the second half. Twice, the Bearkats cut the margin to four - on a three basket by Konner Tucker to make it 33-29 at 17:55 and on a jumper by Marcus James at 14:30 as SFA led 38-34.
Sam Houston could come no closer as SFA went on a 13-1 run to take a 50-34 lead at the 9:57 mark. Stephen F. Austin's largest lead was 22 points.