The home fans were unhappy with referee David Webb for allowing a couple of strong pushes on Gornell and Zoumana Bakayogo to go unpunished.
In between the groans, the busy John Welsh chipped a 25-yard shot narrowly over the bar.
Mr Webb could not ignore a late challenge by Alan McCormack on Gareth Edds that earned the Southend midfielder a yellow card. Right-winger Francis Laurent went into the book on 47 minutes for aiming an off-the-ball kick at Goodison.
Southend, a tall and powerful side, threatened from a couple of set plays late in the half and Edds did well to clear one ball under the crossbar.
Tranmere went close to doubling their advantage just before the break when the visitors struggled to clear a corner and in the scramble that followed, Edds poked in a close range shot that was deflected just wide of the target by a defender’s boot.
The home side went close again a minute after the restart when Shuker sent Craig Curran darting through the inside left channel to fire a low shot from the edge of the box where Steve Mildenhall turned away at full stretch.
Soon afterwards Shuker played the galloping Bakayogo into a similar position and the full back fired wide of the near post.
Southend threatened on the break after 55 minutes when Laurent, overstretching as he ran into the box, lifted a shot over the bar.
Goodison finally had to give into his back injury on 64 minutes. The skipper’s departure saw Ash Taylor drop back into the heart of the defence with Paul McLaren taking over in midfield.
Tranmere were indebted to goalkeeper Luke Daniels for a sprawling close range save that kept out Adam Barrett’s header.
The value of Daniels’ intervention was underlined by a second Tranmere goal on 72 minutes by Gornell.
When full-back Shaleum Logan swept in a cross from deep on the right, Gornell’s first headed attempt was blocked by the body of goalkeeper Mildenhall. But the striker seized on the rebound to drive a sharp shot into the far corner from 10 yards.
Tranmere were then grateful to see a first time volley from McCormack and a header by Sean Morrison just miss the target.
TRANMERE: Daniels, Logan, Goodison (McLaren 64), Broomes, Bakayogo, Taylor, Welsh, Edds, Shuker (Thomas-Moore 75), Gornell, Curran. Subs: Collister, Cresswell, Bain, Ricketts, Barnett.
SOUTHEND: Mildenhall, Francis, Morrison, Barrett, Malone, Laurent (Walker 77), Christophe, McCormack, Moussa, Barnard, Freedman (Scannell 69). Subs: O’Keefe, Asante, Bentley. Booked: Tranmere’s Broomes, Southend’s Morrison.
REF: Mr David Webb. ATT: 4,317.
