Jordan Eglseder added 11 for the Panthers (14-8, 6-5 MVC), who have beaten Southern Illinois five straight times at home.
Northern Iowa led 65-61 with 36 seconds left, but Southern Illinois' Matt Shaw went to the line with a chance to bring the Salukis within two. He missed both free throws, and Wesley Clemmons was called for travelling on Southern Illinois' next possession.
The Panthers, who sealed the win at the free throw line down the stretch, shot 29-of-40 from the line. Northern Iowa led 36-29 at halftime and pushed its edge to as much as 62-52 on a dunk by Eglseder with 5:13 left.
Randal Falker had a game-high 21 points to lead Southern Illinois (11-11, 6-5), which had won four of its last five.