The 56-year-old was relieved of his duties on Sunday having failed to guide the Shrimpers into the League Two play-off places, but will return to the dugout for the April 7 clash with Crewe at Wembley.
Sturrock's replacement, who is widely tipped to be former Hull City boss Phil Brown, will manage Southend's next two fixtures against Bradford and Fleetwood but will temporarily step aside for cup final day.
|AGAINST ALL ODDS
|6/5||Southend are 6/5 to win the Football League Trophy with Bet365|
In a statement on the club's official website, Martin also described parting with Sturrock as, "[a] very hard call, but one I instinctively know is correct.
"Our investment has enabled the manager to build a squad both last year and this year, having more quality players at his disposal than most teams in the league.
"As chairman my responsibility and focus must also be on the wider interests of Southend United. The primary objective last season and again this season was promotion.
"The manager and players have understood that from the outset. We came up short last season in the play-offs and the recent results against relatively low league teams have not been good enough."