Jeff Lebo's club got 21 points from junior guard DeWayne Reed, who also led the Tigers on Friday.
Korvotney Barber scored 11 points and added 10 rebounds for the Tigers in the game at the Sears Centre.
Auburn fell to 3-3 with the loss while the Panthers improved to 4-1.
Auburn made just 40 percent of its field goals, compared to 53.7 for the Panthers, who hit 8-17 threes while Auburn made 8-27.
Tigers had 11 turnovers, five less than the Panthers, and held a 31-30 rebounding edge.
Auburn made an 18-6 run after falling behind 11-7 to start the game and built the lead to 28-20 with 3:18 in the first half. However, at halftime the score was tied 28-28.
Northern Iowa went on a 10-0 run in the second half to take a 44-34 lead, but the Tigers cut the lead to 46-44 at 10:55 left with eight points from Reed.
The Panthers stretched the lead to 58-49 with 2:27 to play and held on for the victory.
Jordan Eglseder recorded a double-double for Northern Iowa with 10 points and 10 rebounds. Ali Farokhmanesh scored a team-high 14 points and Johnny Moran added 13 points.
"Jordan Eglseder is gigantic," Lebo said. "He is gigantic. He is 7-foot-1, 290 and we didn't do a good job on him. They shot the ball well from three, and when we helped off inside, they made shots. Our problem is offensively. We can't manufacture any points."
Auburn returns to action Wednesday at Xavier at 7 p.m. CST in Cincinnati and the game will be televised by CBS College Sports.