The goals were the Beninese striker's first since the opening day of the season and they helped the Terriers, who started the day in 16th place in the Premier League table, leapfrog their visitors and climb into 11th place.
Albion meanwhile - now without a win in five matches themselves with three defeats and two draws - dropped a place to 13th in what was an uncharacteristically poor display, which could have easily been a much higher scoreline.
The visitors were 2-0 down at half-time both as a result of, or soon after, corners and they could have no complaints at the scoreline, having registered just one off-target shot and seeing 41 per cent of the ball.
There was little change in the second half with the Seagulls having goalkeeper Mathew Ryan to thank as England manager Gareth Southgate watched on from the stands with his notebook in hand.
In truth, Albion could have had no complaints if the scoreline had been more heavily against them as they were forced into last-ditch defending for the majority of the second 45 minutes.
Chris Hughton made two changes from the Liverpool defeat last weekend, as Markus Suttner and Ezequiel Schelotto came in for Gaetan Bong and Anthony Knockaert, who did not make the match day squad despite being at the John Smith's Stadium.
The first chance went the visitors' way as Glenn Murray headed a whipped Dale Stephens ball towards the bottom corner and Jonas Lossl produced a decent diving save, but the flag was up for offside.
Ryan then made a smart save down to his left on nine minutes as an awkward Shane Duffy header dropped behind him and Mounie's half volley was creeping into the far corner.
And the hosts led in the 12th minute from another corner. Christopher Schindler flicked on the set-piece and Mounie arrived at the back post completely unmarked to bundle the ball home.
Albion did very little to threaten a leveler with passes in behind the full-backs being quickly cut out, while balls from the back towards Murray proved ineffective.
The Terriers, meanwhile, who had caused problems in the final third with their pacy attacking line, won another corner on the stroke of half-time. Mathias Zanka's deliver was only half cleared, with Aaron Mooy putting the ball back in from the other side and Zanka was able to header the cross into the danger zone for Mounie to nod in his second.
Hughton turned to Solly March at half-time, replacing the ineffective Schelotto, but a couple of nervy moments ensued at the start of second 45 minutes for the visitors.
First, Dunk tracked the breaking Tom Ince all the way into the area and got just enough of a foot on the ball, before a decent block saw away a goalbound effort.
Ince was the next to test Ryan, but the goalkeeper blocked his close-range effort from Tommy Smith's cross and got up to collect the ball as it rolled across the goalmouth. Soon after Mounie blazed over from a cut-back as the Huddersfield attacks kept coming.
Jose Izquierdo replaced Pascal Gross for Albion, who had few meaningful efforts, while at the other end, on 69 minutes, Smith whistled an effort across goal and narrowly wide, before Ince sent one just over the bar.
Despite the plethora of chances, the visitors somehow kept the hosts out for the remainder of the half, with the small positive of not doing more damage to their decent goal difference.
Albion: Ryan; Bruno, Duffy, Dunk, Suttner; Schelotto (March 46), Stephens, Propper, Brown (Hemed 73); Gross (Izquierdo 63); Murray. Unused subs: Krual, Huenemeier, Kayal, Baldock.
Huddersfield: Lossl; Smith, Zanka, Schindler, Lowe; Mooy, Hogg; Quaner, Ince (Lolley 86), Kachunga (Williams 88); Mounie (Depoitre 85). Unused subs: Coleman, Whitehead, Cranie, Hadergjonaj.Referee: Stuart Attwell.