New Southend United manager Phil Brown will manage the club in the Johnstone's Paint Trophy final on 7 April.
The club had said former boss Paul Sturrock, who was sacked last Sunday, would "lead out" the team at Wembley.
But Sturrock told BBC Essex: "I feel unrest caused to the players and fans on this fantastic day might spoil their enjoyment.
"It was obviously a difficult decision, but I do feel it's the right one as a professional man."
The Scot plans to travel with the supporters, ''have a few beers" with them before the game and "enjoy watching my team as a true fan".