Dons skipper Dean Lewington had cancelled out Scott Arfield's first-half opener before Novak's late spot-kick was saved by David Martin, after Gary MacKenzie had seen red for violent conduct.
The Dons started brightly and Shaun Williams had a fierce 25-yard strike pushed over the bar by Ian Bennett before Dean Bowditch saw his deflected shot flash past the post after a slick passing move.
But Huddersfield seized control and Arfield put them ahead after 37 minutes, slotting in the rebound after Alan Lee's header had come back off the foot of the post from Jack Hunt's cross.
The Dons piled forward after the break and Lewington equalised in the 65th minute from a Bowditch corner, ramming in the rebound after MacKenzie's header had been parried by Bennett.
Huddersfield substitute Gary Roberts then had a shot cleared off the line by Luke Chadwick before Novak's late penalty miss, which came after MacKenzie had been shown a straight red card for lashing out at Lee in the box.