Turner, on loan from Everton, had staged a one-man show in the second half to snuff out the Shrimpers as Wednesday capitulated.
But with seconds to go midfielder Jermaine Johnson smashed a shot straight at defender Lewis Hunt's arm as referee Andre Marriner pointed to the spot, substitute Steve MacLean stabbing home the winner for Wednesday's first win of 2007.
Wednesday had fallen behind in the 15th minute. Kevin Maher's corner from the left flank was flicked on by centre-back Spencer Prior and Lewis Hunt bundled the ball over the line.
But the Owls were back on level terms a minute later. After winning a free-kick 20 yards out, midfielder Chris Brunt fired in a stinging shot and Marcus Tudgay stretched to head the ball past Darryl Flahavan from close range.
Southend, who had lost just one of their last seven away games, almost grabbed a second, Mark Gower finding space on the left to slam in a low drive which evaded Turner as full-back Tommy Spurr stuck out a leg to deflect the ball away from the line.
Lee Bradbury headed over as he stretched to meet a Richie Foran cross and Efe Sodje produced a carbon-copy miss as the chances piled up for Southend.
Wednesday caught them on the break on 29 minutes after Sodje blundered letting in the lively Tudgay whose vicious low strike was hammered into his own net in spectacular fashion by Prior as he tried to clear.
Wednesday turned the screw but let shaky Southend off the hook as the chances piled up with Johnson, Tudgay, Brunt and Deon Buron squandering the lot.
Southend took a stranglehold on the game after the interval and grabbed their second in the 61st minute, Gower threading the ball to Freddy Eastwood who coolly rounded Turner on the edge of the area and slotted the ball into an empty net.
Wednesday caved in as Southend moved in for the kill but were met by the defiant Turner as he snatched a Gower shot, foiled Foran, stretching out a foot to deflect his low strike, before producing two more stops to deny the impressive midfielder.
Johnson carved out Wednesday's winner two minutes into stoppage time. His shot slammed against Hunt's arm as the referee pointed to the spot and MacLean drilled in a dramatic winner.