The striker slotted home a loose ball in the 51st minute to cancel out Colin Larkin's 24th minute opener for Northampton.
Southend had the first chance when Mark Gower fed striker James Walker, but his 16-yard effort flashed wide with Mark Bunn beaten.
Northampton appealed for a penalty after Larkin appeared to be brought down by Peter Clarke, but referee Darren Deadman waved away the midfielder's appeals.
Minutes later the Cobblers breached the home defence when lone forward Adebayo Akinfenwa fed Ryan Gilligan as he burst into the box.
However, his 16-yard half volley was easily held by Darryl Flahavan.
Gilligan's corner from the right was met by an unmarked Larkin at the near post and he headed the ball into the bottom left-hand side of the goal to break the deadlock.
Mr Deadman again turned down Southend appeals for a penalty when Barnard went down under a challenge from Northampton skipper Chris Doig.
Six minutes into the second half, promotion-pushing Southend got back on terms as Charlie Mulgrew saw his 30-yard free-kick from the right channel turned on to the bar by Bunn.
The ball bounced off the bar and into the path of Barnard, who slotted home for his eighth goal in 10 starts for Blues.
Eight minutes later, only an acrobatic one-handed save from Bunn stopped the Cobblers slipping behind as he denied Southend skipper Adam Barrett a close-range header after he was picked out by Mark Gower on the left.
Daniel Jones then came to Town's rescue when he cleared Tommy Black's shot from an acute angle off the line after the Southend winger had been put through by Alan McCormack.
Walker saw a looping effort rebound off the crossbar before Gabor Gyepes came close to bagging a winner for Town, but his header from a Jones free-kick flew just over the bar.