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.
Michigan coach Jim Harbaugh said Tuesday he has informed competing quarterbacks Jake Rudock and Shane Morris of his decision on a starter for the Wolverines' opener Thursday night at Utah.
No. 5 Michigan State will start redshirt freshman Vayante Copeland at one of its two cornerback spots Friday night at Western Michigan.
Less than four months removed from his transfer to Florida State, Everett Golson has been named the Seminoles' starting quarterback.
After hinting at it for more than a week, LSU coach Les Miles confirmed Monday that Brandon Harris will start at quarterback in Saturday's opener against McNeese State.
USC AD Pat Haden said he had "thoughtful conversations" with medical professionals and that "a lot of careful thought was given" before deciding on a course of action for coach Steve Sarkisian.
A final decision in Ohio State's quarterback derby won't be revealed until just before the season kicks off, but Urban Meyer isn't ruling out playing both his decorated candidates.