Huddersfield had won five and drawn one of their first six matches but a goalkeeping error from Danny Ward gifted Brighton a late win.
Mooy, who scored at the weekend against Leeds United, was unable to repeat his heroics. He did manage to complete an equal-game-high 76 passes as well as four tackles and three interceptions.
With the score locked at 0-0 in the 80th minute Anthony Knockaert produced a shot that took a slight deflection that Ward was unable to hold on to.
It brings to an end Huddersfield's best start in their 108 year history, although they still remain top of the table, one point above Newcastle who beat Queens Park Rangers 6-0.
Australia's Massimo Luongo was left out of the squad by QPR manager Jimmy Floyd Hasselbaink.
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