The day had started poorly for Town when, with all eyes on highly rated Bobby Zamora, Lee Steele showed that Brighton were not a one-man team with two chances in the first half.
Steele outpaced Nathan Clarke and forced Margetson to tip his low effort away in the ninth minute.
Seven minutes later Steele was in another shooting position but didn't test Margetson.
The start had been generally quiet but the visitors looked comfortable on and off the ball which didn't bode well for the Terriers who could have taken the lead through Andy Booth when Danny Schofield knocked the ball down for him. Booth missed his chance from an awkward angle and Brighton took full control of the game.
The 34th minute saw John Thorrington dispossessed at the edge of the Town area and Lee Steele was through on goal again but he failed to spot Richard Carpenter unmarked in a great shooting position and his chance went to waste as Carpenter bayed for the ball.
Bobby Zamora ensured that the goal that they deserved was scored, though, when he took control of a long ball shortly afterwards, beat a defender, and struck a beauty past Margetson.
Zamora forced another save from Margetson minutes later and it was clear that the Seagulls held the upper hand in the first half.
Town were wasteful with the few chances they got. Danny Schofield went down on the edge of the Brighton area but Kenny Irons' free kick was well saved by Kuipers.
The second half was a supreme show of pressure from Brighton against a Town side who had started defending deep again and it wasn't long before Chris Holland's goal line clearance was followed by Gary Hart's low strike to make it 2-0 in the 61st minute.
Not content with 2-0 Brighton could have made it 3-0 but for a one handed save by Margetson from Lee Steele and a classy tackle on the line by Nathan Clarke for the clearance.
With things looking very bad for Town they got a lucky break with a free kick in a promising position for Kenny Irons in the 72nd minute.
The experienced Town midfielder didn't wait for the otherwise excellent Michels Kuipers or his defenders to get ready before he unleashed the drive which defeated him.
The goal sparked the start of a belated Town mini-revival which brought chances for Chris Holland and Andy Booth to score the equaliser but, for luckless Town, there wasn't enough time to score against a Brighton side who richly deserved the points on their earlier display.
Town (4-4-2): Margetson, Jenkins, Evans (Heary 46), Gray, Clarke, Irons, Thorrington, Mattis, Holland, Booth, Schofield
Subs not used: P. Senior, Moses, Macari, Hay
Booked: Jenkins, Thorrington
Scorer: Irons 72
Brighton (4-4-2): Kuipers, Watson, Mayo, Cullip, Morgan, Hart, Oatway, Brooker (Jones 88), Carpenter (Rogers 78), Steele, Zamora
Subs not used: Pitcher, Crosby, Pethick
Booked: Mayo, Morgan
Scorers: Zamora 34, Hart 61
Attendance: 10,727 (1,331 Away)
Referee: Uriah Rennie (Sheffield)
Read Mel Booth's full match report on Monday.
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93 mins: Andy Booth headed over from Clarke's ball in.
92 mins: Thorrington was penalised for offside - he took exception to the decision and was booked.
90 mins: Thorrington's drive was too slow and Kuipers picked up the ball easily.
89 mins: 2 minutes of added time were indicated.
87 mins: Oatway shot high with the game petering out.
85 mins: Holland's early pass was too far away for Thorrington to reach.
84 mins: Zamora cleared from Irons' set piece.
83 mins: Andy Booth tried to barge through the Brighton defence but made no headway. Moments later Mayo brought down John Thorrington who had darted past on his way to goal as a third striker.
80 mins: Steele's left footed shot was high and wide after Hart had put him through follwoing Zamora's run.
79 mins: Schofield closed down Kuipers and forced him into a hurried clearance.
76 mins: Holland's cross was wasted.
75 mins: Jenkins blocked Zamora's efforts to get a shooting chance.
73 mins: Chris Holland's effort was cleared off the line by Kuipers after another Thorrington run. Suddenly Town had started to play again.
72 mins: Kenny Irons struck his free kick clean and early and it beat Kuipers to put the Terriers back in the game.
67 mins: Margetson made another one handed save from Steele and Clarke's classy tackle on the line saved Town from another possible goal.
66 mins: Zamora was bodychecked by Steve Jenkins - who just stood in Zamora's way. Uriah Rennie had already booked Jenkins minutes earlier and let the Welshman off with a lecture.
65 mins: Chris Holland headed over the bar after a great ball by Thorrington found the midfielder in plenty of space.
61 mins: Gary Hart made it 2-0 with a low strike into the corner of the net after Town's defence invited attack by dropping deep again.
60 mins: Chris Holland cleared off the line from Danny Cullip after disarry in Town's defence.
59 mins: Thorrington broke free at speed but he didn't see Schofield in space and his one man attack eventually broke down.
58 mins: Steele's flicked header was beaten away by Margetson.
55 mins: Kuopers saved from Booth after the big striker had beaten the offside trap.
52 mins: Mayo's effort was overhit and went for a goal kick.
50 mins: Thorrington's corner was caught by Kuipers before Booth could get his head to it. Town were slowly putting some pressure on.
47 mins: Holland made it to the touchline and put a cross in which Andy Booth scuffed into the hands of Kuipers!
46 mins: Thomas Heary was on for the injured Gareth Evans as Town set out to equalise.
HALF TIME: The Seagulls proved tough opponents as they went in at half time separated by quality goal from Bobby Zamora. It could have been more as Lee Steele spurned two early chances and only offered Martyn Margetson a shot to save on his first attempt.
Town's best chance of the half came from a Danny Schofield knockdown for Andy Booth but he could only hit his effort wide from a narrow angle.
46 mins: Kuipers saved from Kenny Irons on the stroke of half time.
45 mins: Schofield was crowded out by some Brighton defenders and was fouled on the edge of the Brighton area into injury time.
42 mins: Irons tried a 35 yard speculator but Kuipers was alert and made the save.
39 mins: Zamora forced another save from Margetson after the referee had played on.
37 mins: Thorrington fired wide with Booth free.
36 mins: Margetson made a superb one handed save from Paul Brooker after Steele had put him through.
34 mins: Bobby Zamora made amends moments later when he gave Margetson no chance with a rasping drive - it was a clinical finish.
34 mins: Thorrington was caught in possession on the edge of the box but fortunately Town cleared after Lee Steele failed to spot Richard Carpenter baying for the ball in a point blank shooting position.
33 mins: Steve Jenkins cleared from Brooker as he tried to find Zamora.
30 mins: John Thorrington was picked out by Holland but the American's cross was poor and was plucked out of the air by Kuipers.
28 mins: Mayo's free kick was headed away by Andy Booth.
25 mins: The game was fairly quiet despite Brighton being on top. Neither keeper had been significantly tested.
21 mins: Nathan Clarke's long throw was passed to Andy Booth by Danny Schofield but Town's talismanic striker couldn't make more of the best chance of the game for Town.
19 mins: Mattis' shot was blocked by Carpenter as Town ejoyed pressure. Schofield flicked a header on but Booth was waiting for the dummy moments later.
17 mins: Brooker slid in and intercepted a Thorrington run. Clarke's long throw was headed away by Mayo for a corner.
15 mins: Steele's shot was wayward as Brighton took control of the early passages of play.
14 mins: Thorrington's run was picked out by Andy Booth but the winger had stayed too wide and there was nobody in the box to receive a cross.
11 mins: Clarke broke up a promising Brighton attack and punted the ball free. Gareth Evans pulled up while trying to put a pass through to Andy Booth. Alex Moreno hurried onto the pitch to look after the injured left back.
9 mins: Booth's turn and pass to put Schofield through was once again deemed offside.
8 mins: Booth headed clear from defence during a Brighton move.
5 mins: A great ball by Booth found Schofield on the run but he was inexplicably flagged offside.
4 mins: Andy Booth's effort flew over the Brighton bar after a steady start for both sides.
Danny Schofield, back from suspension, replaced Chris Hay in the starting lineup while Dwayne Mattis was fit to take his place in midfield after suffering a bad gash in the match against QPR