The Demons remain in third place in the Southland Conference with two games to play.
SE Louisiana led early, but Northwestern State exploded for a 23-point run in the middle of the first half, hitting 8 of 10 shots including five 3-pointers, and the Demons led 44-31 at the break.
Northwestern State (17-10, 12-4) scored the first seven points of the second half - including Matt Killian's 3-pointer - extending the lead to 20. But SE Louisiana scored the next 15 points, including dunks by Devonte Upson and Onochie Ochie, to reduce the deficit to five at 51-46.
But Thompson (18 points) made four 3-pointers and four free throws after that point, and Northwestern State won easily.
Cedric Jenkins led SE Louisiana (9-20, 6-10) with 25 points.