The Huskies had 13 points with 3:21 to play but found their scoring touch late in a 42-25 loss.
Northern Illinois trailed 18-4 at the half after shooting 1 for 31, including 29 straight misses.
Earlier this season, Northern Illinois set the record for fewest points in a first half in the shot clock era with five against Dayton on Dec. 1.
The Huskies' 3.2 percent field goal percentage in the first half Saturday also set a record, breaking Savannah State's 4.3 percent against Kansas State on Jan. 7, 2008.
The lone made field goal also tied a Division I record set by Savannah State in that game.
The Huskies finished the game 8 for 61 from the field for 13.1 percent, another NCAA record.
NIU ended a 24-minute, 32-second drought without a field goal with a layup with 14:27 left to close the Eastern Michigan lead to 23-7.
After his team's 32 misses, Northern Illinois' Daveon Balls finally made a 3-pointer with 2:05 left. The Huskies finished 1 for 33 from long range.
Balls led the Huskies with seven points, all in the final 8:38.
The Huskies narrowly avoided the record for fewest points in a game -- 20, set by Saint Louis in January 2008.