Scunthorpe made the early running with Paul Hayes picking up a ball from striker partner Gary Hooper but firing wide from 20 yards.
Grant McCann then put former Southend striker Hooper through but his shot was turned out for a corner by goalkeeper Steve Mildenhall.
But Southend clawed their way back into the match to test the makeshift Iron rearguard, which was without the first choice back four due to injury and suspensions.
Robinson picked out Anthony Grant's run down the right but the winger's shot was blocked by Joseph Mills.
Francis Laurent then beat the offside trap but saw his effort headed out for a corner by Krystian Pearce.
Blues stepped up the pressure with skipper Adam Barrett's crossfield pass from the left being headed just wide at the far post by Osei Sankofa.
The half finished with Franck Moussa having an effort saved at the foot of the post by Murphy, before Robinson's goalbound header from a Moussa corner rebounded to safety off Blues defender Dorian Dervitte.
Southend's pressure finally told in the 54th minute when a sweet pass from Grant allowed Robinson to beat the offside trap and bear down on goal. Murphy advanced and went down early, allowing the on-loan Watford forward to slot home into the empty net.
Scunthorpe nearly equalised straightaway when Hooper squared the ball to Hayes and he raced into the box only for his shot to be blocked by Mildenhall's legs for a corner.
But Southend went in search of a second goal and saw Grant denied by a diving Murphy before Barrett headed into the side-netting.
However, it took a great save from Mildenhall to keep the scores level after Hooper charged down the right and unleashed a shot under pressure from Peter Clarke.
And Scunthorpe hit the woodwork after Simon Francis gave the ball away and Ian Morris crossed for Hayes to head against the crossbar.
But with three minutes left on the clock Southend grabbed their second goal when Lee Barnard's shot came off a defender and McCormack was on hand to fire into the bottom right-hand corner from six yards out.