Western Illinois (1-2) was trailing 53-49 with 4:01 left when Garret Covington took control, scoring 8 of the last 11 points to give the Leathernecks their first lead since the 10:51 mark, when they were ahead 39-38.
Covington, who finished with 29 points, slipped in for two layups and made four free throws to set up Batish's game-winning jump shot.
Covington was 4 of 9 from beyond the arc, making 7 of 15 field goal attempts.
The Lions had a 25-21 lead at the half and held a 53-45 advantage with 6:15 remaining in the game.
Zay Jackson led Southeastern Louisiana (0-3) with 17 points. Joshua Filmore and DeVonte Upson added 10 each.