Barnard was introduced at half-time and made his mark with a cool finish after Oldham went in front through Neil Eardley's penalty.
There was an end of season feel to a match of few real chances, but the result meant more frustration for Latics manager Joe Royle.
His return to Boundary Park after 15 years away has yielded just four points from a possible 24 and Royle admitted sweeping changes will be needed in the summer if Oldham are to challenge for promotion next term.
They have been in freefall since January and the familiar problem of conceding soft goals was again on show for Southend's leveller.
Barnard capitalised with his 11th goal of the season and it was Southend who went closest to snatching all three points.
Southend wasted an early chance when Adam Barrett raided down the left and set up Dougie Freedman, who blazed over the bar.
But Oldham were denied by the woodwork after nine minutes as midfielder Kevin Maher floated a free-kick over the defensive wall and saw it strike a post.
Simon Francis headed wide for Southend before referee Craig Pawson angered the home crowd by refusing penalty appeals for handball.
Oldham's Ian Westlake then scuffed a shot straight at the keeper and went close from 18 yards with a powerful drive on the turn.
Oldham broke through on 51 minutes after Dean Smalley seized possession wide on the left and sprinted into the box before being brought down by Peter Clarke.
The resulting spot-kick was converted by Eardley as he drilled his shot through Steve Mildenhall's dive.
Oldham, however, led for less than ten minutes as men were caught out of position at the back, leaving Theo Robinson in space.
Robinson crossed to Barnard, who controlled eight yards out before drilling inside the posts.
Southend could have gone in front when Francis sent a free header off target, while Anthony Grant's injury-time free kick forced a save from Mark Crossley.