Wolves defender Malone, who was on loan at Roots Hall last season, played as a makeshift left-winger and equalised in the 28th minute when he waltzed through the Southend ranks and fired home from eight yards.
It was the first goal the Shrimpers had conceded at home in 460 minutes, but it had looked a different story when the visitors went a goal behind after only three minutes.
Ryan Hall's corner from the left was headed past goalkeeper Adam Legzdins from six yards by Barry Corr for his 21st goal of the season.
Burton were reduced to 10 men in the 84th minute when right winger Jacques Maghoma was dismissed for directing foul and abusive language at the Southend fans.
And Southend saw substitute Lee Sawyer sent off in stoppage time for a second bookable offence.
Both sides had their chances to win the game but Burton were indebted to Legzdins for a smart double save to deny Blues' top-scorer Corr.