Paul Hayes rescued a point for League One leaders Scunthorpe who stretched their unbeaten run to 12 games.
Hayes converted a 79th minute penalty to make up for two earlier misses.
Earlier Southend had taken a second-half lead when Lee Barnard headed home a corner to score his sixth goal of the season.
Scunthorpe's Gary Hooper headed wide of an open goal in the first-half while defender David Mirfin also nodded over from a corner, before Hayes equalised.
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