Harnish threw for three TDs in the opening 18 minutes as the Huskies (1-0) took a 28-6 lead on the Black Knights (0-1).
The win was Northern Illinois' first over a service academy in four tries. The Huskies dropped a 21-14 decision at Army in 1992 and lost both games of a home-and-home series with Navy in 2007 and 2008.
Huskies' tailback Jasmin Hopkins rushed 14 times for 138 yards.
Doeren, a former Wisconsin assistant, took over as Northern Illinois head coach last December following Jerry Kill's departure for Minnesota.
Harnish also ran for a touchdown and he capped his day with a 4-yard toss to Martel Moore that put NIU up 49-6.
Army scored three straight TDs in the fourth quarter.
Doeren became the first head coach to win a Northern Illinois debut game since Jerry Pettibone's 1985 squad beat Western Michigan 17-0.
Jamal Womble, Martel Moore, Akeem Daniels, Nathan Palmer and Luke Eakes each caught touchdown passes for the Huskies, who set a school record for wins by going 11-3 last season.
Army coach Rich Ellerson, opening his third season, guided the Black Knights to a 7-6 record in 2010 and their first bowl victory since 1985. Army beat SMU 16-14 in the Armed Forces Bowl.
Army falls to Northern Illinois, 49-26
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