Toledo was up 81-79 with a minute to play when Baker and Anthony Johnson sank consecutive 3s to put the Huskies back on top, and the Rockets' Julius Brown missed a 3-pointer at the buzzer to give Northern Illinois the win.
Baker finished with 6-of-13 shooting from the field for the Huskies (11-15, 5-10 Mid-American Conference). Aaron Armstead added 15 points.
A trio of 3-pointers by Baker within the first four minutes helped put the Huskies on top early and they led 41-34 at the break.
Brown led Toledo with 20 points.