The victory was only the third that Hughton has achieved against the Arsenal manager and all have come with a different club.
Allardyce achieved this feat last season with Crystal Palace, after previously steering Bolton Wanderers and Blackburn Rovers to victory over Arsenal.
Hughes has managed four clubs to victory against Wenger: Blackburn, Manchester City, Queens Park Rangers and Stoke City.
The 2-1 win that Hughes oversaw for QPR in March 2012 is also significant because it was the last time Arsenal had lost to a side promoted to the Premier League that season.
Brighton ended a 35-match unbeaten run by Wenger's team against promoted sides on Sunday.