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  Heneghan's early near-post header from Peter Winn's free-kick made it 1-0.
  Southend equalised when Barry Corr's penalty found the bottom corner after John Rooney had fouled John White.
  But winger Mahon won it on 51 minutes when he cut in off the right flank to fire home from the edge of the area.
  Mahon's stunning left-foot shot earned Steve Burr's Chester a place in Monday night's televised second round draw for the first time in eight years.
  It is a level of the competition the reformed club have not reached since a team including Everton boss Roberto Martinez and Stoke City striker Jonathan Walters reached the third round in January 2007.
  But Chester, 14th in the Conference, were good value for their victory against the Shrimpers, who stand seventh in League Two.
  Burr's men, in fact, could have won by more, but Southend keeper Daniel Bentley made a good first-half save to deny Craig Hobson's low 18-yard shot and Rooney, younger brother of Manchester United and England captain Wayne, had an effort cleared off the line by Gary Deegan.
summary: Ben Heneghan and Craig Mahon got the goals at Roots Hall as Conference side Chester produced the FA Cup first-round shock of the day by beating Phil Brown's Southend United.