A searing volley brought a fifth goal in as many games for the Sheffield Wednesday loanee.
His right-footed strike was misery for Bristol Rovers as their hopes of a first home win were snatched away once again.
Southend, hoping for a quick return to the Championship, went behind to an early penalty and took time in the non-stop drizzle to wind up their game.
They did so as they dominated the second half but Rovers, after shipping eight goals in three home games, defended as if their careers depended upon it.
Their penalty came after just 11 minutes when Garry Richards handled a shot from Rovers centre-back Steve Elliott and Richard Walker placed the spot-kick carefully to the keeper's left.
Walker has yet to score from open play, but this was his fourth from the penalty spot.
The joy in Rovers camp was qualified for on the two previous occasions they had been given early penalties, they had lacked the defensive know-how to hold on.
Their lead was quickly under threat as headers from Adam Barrett, an ex-Rovers captain and the predatory Clarke had defenders scrambling to boot to safety.
Southend's winning run of four games had stoked their confidence and once they had settled down they descended aggressively on the home goal.
Rovers had a chance to stretch their lead just before the break when Elliott, having gone up for a corner, saw his header cleared from under the bar by Richards.
Barrett who had been given a warm reception by the fans felt similarly robbed later by an alert jump from Ryan Green.
Southend, driven on from the midfield by Kevin Maher, went close to an equaliser as their captain he bent a free-kick just the wrong side of a post, but it left Clarke to perform the late heroics.