Marin Maric had 11 points and 13 rebounds for the Huskies, which built a 10-point lead at halftime and withstood a late charge from the Flames.
Northern Illinois (10-2) led by seven with 3:03 to go, but a Dikembe Dixson 3-point play cut it to three with 58 seconds left. Baker made 7 of 8 from the line in the last 49 seconds to ice it.
Marshawn Wilson had 11 points and Chuks Iroegbu added 10 for Northern Illinois.
Dixson finished with a career-high 28 points. The freshman has scored in double figures in eight of his 11 games. Tai Odiase scored 13 points and Jake Wiegand added 10. The Flames made 4 of 15 3-point attempts.