Todd threw three touchdown passes to Darvin Adams for the Tigers (7-3), who scored on six of their first seven possessions to jump out to a 42-3 halftime lead. Todd's other scoring pass went to Mario Fannin, who finished with 60 yards rushing.
The Paladins (4-5), a Football Championship Subdivision team, scored 28 points in the second half against Auburn, which played most of its reserves during the half.
The Tigers, who won their second in a row, started the season 5-0 and then suffered three losses before rebounding with a win over Ole Miss last week.
Adams caught six passes for 115 yards for Auburn. Anthony Gulley rushed for 77 yards and Ben Tate added 75 yards rushing for the Tigers, who also totaled 282 yards on the ground.
Tate has rushed for 1,142 yards this season and is 13th on Auburn's single-season rushing chart.
Jerry Williams rushed for 35 yards and 2 touchdowns for the Paladins and also caught four passes for 42 yards.
After a 23-yard Matthew Cesari field goal for Furman, Auburn stretched its lead to 14-3 on a 9-yard run by Tate after an 80-yard drive.
On Auburn's next possession, Todd completed a 24-yard scoring pass to Fannin. Adams caught scoring passes of 23 and 41 yards on Auburn's first two possessions of the second quarter and Tate had a 5-yard scoring run with 41 seconds to play before halftime.
The Paladins were able to make the game interesting in the second half as Auburn emptied its bench. Furman's first touchdown came on a 6-yard run by Williams after an Auburn fumble deep in its own territory. Tersoo Uhaa had a 19-yard scoring run for the Paladins on their next possession.
Gulley scored his first two career touchdowns for the Tigers in the fourth quarter on runs of 13 and 50 yards. Gulley is normally a wide receiver but saw time at running back and defensive back in the blowout.
The outmatched Paladins did not give up and continued to play hard in the final seconds, scoring on 17-yard pass from Chris Forcier to R.J. Webb with 21 seconds to play.
The win assures Auburn, which became bowl eligible last week, of a winning season.