Raven Lee had 11 of his 14 points in the second half for Eastern Michigan (17-10, 6-8 Mid-American), which led by as many as 19 in the first half.
Northern Illinois (10-15, 4-10), which trailed 40-24 at halftime, used a 15-4 run to pull within 46-41 with midway through the second. Two free throws by Aaron Armstead cut the Huskies' deficit to four with 3:12 remaining.
Brandon Nazione answered with a three-point play and Eastern Michigan made 10 of 14 free throws in the final 1:38 to seal it.
Anthony Johnson led Northern Illinois with a career-high 23 points.
There were 58 fouls and the teams combined to shoot 75 free throws.
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