The strike gave the visitors their first win after three successive league defeats, while Leyton Orient's promotion dreams took another battering with their third successive home reverse.
The first half was largely an insipid affair with both sides struggling to create clear openings.
Home striker Jabo Ibehre ended a fine run with a tame shot, but it was the visitors who should have gone ahead on 12 minutes when Malvin Kamara sent in a perfect cross, but striker Phil Jevons unbelievably headed wide from close range.
Kamara, always a handful down the right, tried his luck from a tight angle but Orient keeper Glenn Morris was equal to the effort.
Just before half-time Kamara set up Chris Brandon, but his effort flew over the stand and out of the ground.
While Orient came back with a late flourish and Jason Demetriou curled two efforts just wide.
After the break Demetriou fired in another effort from 18 yards that Town goalkeeper Matt Glennon did well to push away.
But the visitors always looked dangerous on the break and twice Robbie Williams tested home keeper Morris.
But it was Orient's leading scorer Adam Boyd who should have put the home side ahead on 70 minutes. On as a sub for Wayne Gray, he tapped the ball wide after good work by Aiden Palmer and JJ Melligan.
It proved to be an expensive miss as Huddersfield wrapped up the points 13 minutes from time. Beckett, on as a 71st minute sub for Jevons, headed a good chance wide within two minutes of his arrival.
But he was on hand to fire home Andy Booth's right-wing cross five minutes later to give his side the victory they deserved.