A goal from Lee Novak - a former target for the Iron under former manager Nigel Adkins - gave the Terriers all three points, securing a play-off place for them.
Scunthorpe remain on 50 points, but Wycombe's defeat at champions Charlton means only Yeovil and Leyton Orient can be caught by any of the bottom four.
"Thank God! I always felt that in the second half of the season we were capable of being higher up the league," said Knill.
"The 10-match unbeaten run did it for us. It came at just the right time and the players should take some credit for that. We don't want the same start to next season as we had this time."
The Terriers have been tough to beat for much of the season, and Knill pointed to two Bobby Grant efforts which hit the woodwork, along with a Jimmy Ryan attempt that grazed the bar, as evidence his side did not deserve this defeat.
"I was pleased with our performance and thought we were worthy of all three points," he said.
"Everything we asked the players to do they did. We knew we needed to keep possession and pass the ball and we did everything but put the ball in the back of the net.
"We knew Huddersfield were a good side and the longer we kept the ball the less chances they would have, and it worked."
Simon Grayson, Hudds boss, said his side's poor form - they had lost their three outings prior to facing the Iron - will not put them at a disadvantage as they head into the play-offs.
"It's a lottery. It doesn't matter what happens before, it's what you do in the play-offs themselves that counts," he said.
"I have been involved in teams that have finished third, fourth, fifth and sixth as a player and a manager with different outcomes.
"There's no right or wrong way to get there and once there it's a lottery. Ultimately it's how you end up that matters.
"Our results have been disappointing but this was a difficult game and we have played a lot better than we have for a few games. The players stuck to the task and we got the result."