Novak struck his 15th goal of the season for the play-off bound Terriers from Gary Roberts' through-ball in the 89th minute of a match the visitors had dominated.
Striker Bobby Grant, just back from a loan spell at Accrington, twice hit the woodwork for Scunthorpe while Jimmy Ryan also struck the post.
Grant, who scored three times in eight games for Stanley, struck the post with a long-range free-kick after 27 minutes after Diego Arismendi had fouled Cliff Byrne.
The 21-year-old also worked an opening in the 67th minute that saw Ryan graze the upright with a tame shot, while Grant also hit the bar with a shot in the 78th minute.
Huddersfield rarely threatened until late on and Jordan Rhodes' 'goal' in the 75th minute was ruled out for off-side before Novak's last-gasp winner.
