Boro dominated possession and had far more chances than their opponents.
The Terriers will rue the fact they have now lost ground in the race for the play-offs, as Carlos Coberán's side offered very little over the course of the game.
Watmore scored two goals in quick succession, turning in two crosses to put his side 2-0 up.
Story of the match
Marcus Tavernier saw a lot of the ball early on in the game, as his cross aimed for the far post went straight at the first man.
Danny Ward had a chance to give the Terriers the lead as the ball was fed through to him to play him in on goal, but he couldn’t quite get on the end of the pass.
There was a scramble in the visitors' box which saw the ball fall to Harry Toffolo, but he was only able to scuff his shot wide.
Middlesbrough capitalised on Huddersfield’s missed chances soon after, as Duncan Watmore found himself with time and space after getting on the end of a cross from the right-hand side.
He smashed the ball first time past Lee Nicholls to give Wilder’s side the lead in the 16th minute.
Watmore doubled the visitors’ lead in similar fashion in the 22nd minute, this time lobbing Nicholls from a cross with a beautiful finish. Boro had played some fantastic football in the early stages of the game and deserved their lead.
The former Sunderland forward nearly had a hat-trick 26 minutes in when he raced through on goal, but his effort was straight at Nicholls.
Duane Holmes looked to pull a goal back for the hosts from the edge of the box, but his shot went high and wide.
Watmore skipped some challenges and got to the by-line, but elected to shoot instead of cutting the ball back for a teammate, which likely cost the visitors a great chance to make it three.
The half went from bad to worse for Huddersfield when Matthew Pearson went off injured for the hosts. He was replaced by Ollie Turton.
Watmore cut the ball back to Andraž Šporar who had his shot blocked from about eight yards out just before the interval.
Wilder was on course for his first win as Middlesbrough manager at the break. His side had dominated possession, been clinical in attack and solid defensively and in the first half Coberán and his side had no reply.
Half time score: Huddersfield 0-2 Middlesbrough
Tavernier had a one on one soon after the restart to make it 0-3, but Nicholls made a smart stop to keep it out.
Watmore stretched to connect with a cross, but his header could only force a comfortable save from the Terriers' keeper.
He combined with Šporar again minutes later, once again cutting the ball back to the Slovenian, whose shot whistled past the post.
Around the hour mark, Huddersfield gained a bit of momentum of their own in the game, enjoying a lot more of the ball for a spell in the game.
Daniel Sinani had an effort for the hosts from just outside the box which crept wide.
Isaiah Jones had a brilliant chance to seal the win for Wilder's side in the 66th minute, as he was picked out by a cross that he could not connect with. How Boro had not got a third in the game was a mystery as the game headed into the final stages.
Šporar had another chance to score, but he fired well over from the edge of the box.
Boro appealed for a penalty with 12 minutes left to play, as Tavernier's shot appeared to be blocked by the hand of Tom Lees, who had both of his arms raised. However, the referee waved the appeals away.
The Terriers had a late goal back somewhat fortuitously, as a cross hit Hernandez who was tracking back for Boro and caught keeper Luke Daniels out at his near post, giving Huddersfield a late consolation goal.
Boro were far the better side and thoroughly deserved the three points they left The John's Smith Stadium with on a cold Saturday evening in West Yorkshire.
Huddersfield: Nicholls, Toffolo (Koroma 73’), Pearson (Turton 37’), O’Brien ©, High, Thomas, Holmes (Campbell 60’), Sarr, Sinani, Ward, Lees.
Middlesbrough: Daniels, Dijksteel, Tavernier, Sporar, Howson ©, McNair, Watmore, Bamba, Crooks, Bola, Jones (Ikpeazu 88’).
Referee: Thomas Bramall.