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Ellis headed an effort clear from Southend striker Bilel Mohsni in the 70th-minute, who twice went close in the space of as many minutes.
Seconds earlier the Shrimpers' targetman broke free only to be denied by a superb save from Bobby Olejnik, who was quick off his line to save as the visiting forward let fly from the edge of the box.
Both sides hit the woodwork in the first half, with Southend midfielder Ryan Hall's measured free-kick from 25 yards bouncing off the top of the crossbar.
Torquay made most of the early running with recalled forward Ryan Jarvis, on loan from Walsall, heading on to a post following a corner from the left.
In a cagey match the first shot on target fell to Southend striker Neil Harris but it was saved by Olejnik. Jarvis went close with a thumping 47th-minute strike that dipped just over the bar.
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