The result means that Oxford stay a point clear at the top of the table and are still undefeated away from home in the league.
Kevan Hurst's goal before the break appeared to be enough for Southend to pick up maximum points at Roots Hall Stadium, but Matt Richards struck home from the penalty spot in the fourth minute of injury time to deny the Shrimpers a win.
Southend move to 33 points, same as many as second-placed Chesterfield, who take on Newport County away from home on Sunday.
Rochdale and Burton Albion have the same number of points and are in the playoff spots. While the former drew 0-0 with York City away from home, the latter beat Plymouth Argyle 1-0 at Home Park, thanks to an early strike from Adam McGurk.
The win helped Aidy Boothroyd's side climb off the bottom of the standings, but they are still two points from safety.
Results in full: Bristol Rovers 3-0 AFC Wimbledon, Dag & Red 2-0 Wycombe, Exeter 2-2 Bury, Fleetwood 1-1 Oxford United, Hartlepool 1-1 Oxford United, Hartlepool 0-0 Portsmouth, Mansfield 1-2 Morecambe, Northampton Town 1-0 Accrington, Plymouth 0-1 Burton Albion, Scunthorpe 3-1 Torquay, Southend 1-1 Cheltenham, York 0-0 Rochdale