Substitutes Jason Price and Iain Hume inspired Tranmere to victory after they trailed at half time.
Huddersfield went ahead in the 44th minute with loan striker Scott McDonald from Southampton blasting home from close range after chesting down a cross by ex-Rover Kenny Irons.
The Mersysiders were unlucky in the first half. Jason Koumas fired wide when clear, Ian Sharps saw an effort headed of the line by Kevin Sharp and Simon Haworth brought a good save from Scott Bevan.
McDonald went close to adding to the town lead.
But then Jason Price was sent on be Tranmere in the 67th minute and four minutes later netted with a close range shot after Bevan pushed out an effort by Hume.
Then Hume who had come on at the start of the half provided the cross for home skipper Kevin Gray to volley home a left foot winner against his former club in the 77th minute.
"I'm not renowned for my goal scoring but it was not a bad time to score my first for Tranmere against my former club," said Gray. "We got a kick up the backside at half time but after we got the first goal I always believed we would go on and win"
Tranmere caretaker manager Ray Mathias said "I'm pleased with the points but not the performance. We stuttered throughout the game really."
Mathias revealed Alan Navarro who was forced of in the opening period had suffered knee ligament damage Town boss Mick Wadsworth said: "We played great football and got nothing for it and the worry is I don't think we can play any better. We're going to have a lot of catching up to do."