Beane made a 3-pointer and Southern Illinois led 70-59 with 1:35 remaining. Klint Carlson, Matt Bohannon and Paul Jesperson each made 3-pointers as part of a 13-3 run that pulled Northern Iowa to 73-72 with 12 seconds to play.
Beane dunked with three seconds left, sealing the fifth-straight win for Southern Illinois (13-2, 2-0 Missouri Valley).
The Salukis led 39-30 before Northern Iowa used a 16-11 spurt to pull to 50-46 with 12 minutes to go. Beane answered with two 3s and Sean O'Brien added four points to stretch Southern Illinois' lead to 60-48.
The Panthers cut the deficit to six points with 4:28 remaining. Carlson sparked the rally at the 1:10-mark.
Wes Washpun led Northern Iowa (9-6, 1-1) with 19 points.