An uneventful first half finally came to life in the 32nd minute when Bilel Mohsni’s headed strike was ruled out for a push on Oldham goalkeeper Alex Cisak.
The visitors made the most of the decision, and took the lead in the 38th minute when Lucas Scapuzzi’s shot was parried by Luke Daniels and Shefki Kuqi squared the loose ball to James Wesolowski, who rifled the ball home from just outside the box.
Southend brought on Neil Harris and Blair Sturrock up front but Oldham went close when skipper Dean Furman’s 18-yard effort hit the bar.
However, the npower League Two leaders equalised in the 67th minute when Cisak ran out to clear a Sturrock centre and the ball fell to Ryan Hall, who blasted into the empty net from 35 yards.
Cisak made amends by saving from Hall, Mohsni, Peter Gilbert and Phillips, while Mohsni had a second headed goal ruled out for offside in the 89th minute.