The FA said in a statement on Tuesday that a three match ban had been overturned after an independent regulatory commission accepted that the Egyptian had been wrongly dismissed for violent conduct.
Arsenal won the match 3-2, with Elneny sent off for appearing to push Southampton's Cedric Soares in the face during a break in play. Saints' Jack Stephens was also dismissed for a separate incident in a wild last few minutes.
The red card was the first Elneny, 25, had received in his professional career.
The Londoners are 13 points behind the top four, their hopes for the remainder of the season resting on the Europa League, in which they take a 4-1 lead to CSKA Moscow for Thursday's quarter-final second leg.
They play at Newcastle United in the league on Sunday, followed by games at home to West Ham United and away at Manchester United.
(Reporting by Alan Baldwin, editing by Christian Radnedge)
