The 18-year-old, on loan from Stoke City, ended Rovers' run of three successive away defeats this term to leave Huddersfield still without a home win.
Huddersfield could have been at least 3-0 up in the first half but they allowed Tranmere back into the game before the break and fell apart in the second period.
Liam Dickinson, on loan from Derby County, gave Huddersfield the lead when he brilliantly bent a free-kick around the wall in the 16th minute.
At that point Huddersfield were on top and Dickinson almost doubled their lead only to see his flying header go just wide.
Keigan Parker's shot was then blocked by defender Ben Chorley before Dickinson's rebound was saved by Danny Coyne.
Nathan Clarke's point-blank header was tipped onto the bar and over by Coyne as Huddersfield dominated.
Tranmere grabbed a lifeline six minutes before the break when Ian Goodison's ball forward was chested down by Chris Greenacre allowing Edrissa Sonko to volley home.
Tranmere started the second period on top and were first to every loose ball. Four minutes into the second half Rovers scored what proved to be the winner when right-back Shotton rose highest to head home Andy Taylor's free-kick.
Huddersfield boss Stan Ternent switched his personnel twice bringing on subs Danny Cadamarteri, Robbie Williams and Jon Worthington but the team lacked direction or ideas.
Sonko was just off target with another effort before Shotton put Greenacre through. The striker brushed off Clarke and should have scored but steered his finish onto the outside the post.
Chorley had the chance to seal it but flashed wide from a corner and Huddersfield almost snatched an undeserved point when Gary Roberts' angled shot shaved the upright.
Michael Flynn also went close four minutes from time but directed his header wide.