The Salukis scored twice in a 39-second span, with the second touchdown -- the Hill to Allen play -- coming with 21.6 left in the game.
SIU (2-0) made a game of it late as tight end Ryan Kernes caught at 26-yard pass with 1:01 to play that cut the Huskies' lead to 31-28. The Salukis then recovered the ensuing kickoff and marched 57 yards in five plays for the game winner.
Northern Illinois (0-2) led most of the way as tailback Justin Anderson hauled in the first two touchdown receptions of his career and added another on the ground. A sophomore, Anderson scored twice within a 64-second span late in the open half as the Huskies opened a 21-7 lead by halftime.
But the Salukis, behind the passing of Hill, who was 22-of-34 for 245 yards, fought back in the second half. Hill tossed a 16-yard TD strike to wide receiver Allen Turner with 5:49 left in the third. Sophomore cornerback Brandon Williams added a timely 52-yard interception return with 10:30 to play that cut the lead to 31-21.
Kernes lead the Salukis with six receptions for 69 yards while Turner was 4 for 53.
Northern Illinois tailback Montel Clanton led all rushers with 13 carries for 91 yards and a touchdown, but left the game in the third quarter with a knee injury. Anderson had 78 yards rushing on 21 carries and had eight receptions for a game-high 87 yards.
The win was Southern Illinois' first over Northern Illinois since 1979. The Huskies still lead the 76-year rivalry 28-14-1.