Hal Bateman added 14 points and Antonio Bostic had 10 for the Lumberjacks (15-1, 6-0 Southland), who held the Lions (5-10, 3-2) to 26 percent shooting— 16 percent in the second half.
No Southeastern Louisiana player had more than seven points.
The Lions, who had their three-game winning streak snapped, scored 13 straight points in the first half to turn an 18-12 deficit into a 25-18 lead with 2:51 left before the half.
Stephen F. Austin pulled within 25-23 at the break, and opened the second half with a 20-3 run to take a 43-28 lead with 10:04 remaining.
The Lumberjacks are off to their best start since becoming a Division I program in 1987-88, and their best start overall since starting 17-1 in 1985-86.