Lehmann and Phillips charged
The pair were involved in an ugly spat at the end of the game between the two sides on December 29.
German keeper Lehmann was angry with what he thought was rough treatment from Phillips earlier in the game and hurled the ball at the striker right on the final whistle.
The duo had to be separated as the confrontation threatened to explode, as Lehmann felt Phillips deliberately stamped on his foot earlier in the game.
The FA have looked into the incidents and decided to charge the pair with improper conduct, breach of FA Rule E1.
A brief statement on The FA's website read: "The FA has charged Arsenal's Jens Lehmann with improper conduct (breach of FA Rule E1) in relation to an incident involving Southampton's Kevin Phillips at the end of the match between the two teams on 29th December 2003.
"Phillips has also been charged with improper conduct for a separate incident involving Lehmann earlier in the match.
"Both players have until 23rd January to respond."