Freddie Eastwood's ninth goal of the season was enough to take Southend into the second round of the FA Cup.
Eastwood, who later had a goal ruled out for offside, drove a left-foot shot past keeper Ross Fliney on two minutes.
But despite that shock Barnet were on top before the break with Dean Sinclair forcing Bart Griemink into a fine stop.
After the restart Fliney denied Shaun Goater with an acrobatic save while Jason Norville shot wide for the Bees and saw an effort cleared off the line.
Barnet: Flitney, Hendon, Soares (Batt 69), King, Gross, Yakubu, Sinclair, Strevens (Roache 83), Bailey, Hatch (Grazioli 83), Norville.
Subs Not Used: Tynan, Charles.
Southend: Griemink, Hunt, Edwards, Barrett, Wilson, Campbell-Ryce, Guttridge, Maher, Cole (Lawson 85), Eastwood, Goater.
Subs Not Used: Prior, Gower, Pettefer, Smith.
Booked: Eastwood.
Goals: Eastwood 2.
Att: 3,545
Ref: P Armstrong (Berkshire).