Barnard scored 37 league goals in 75 games for the Shrimpers before moving to St Mary's, where he has been out of favour since the Saints' promotion to the Barclays Premier League.
Southend boss Phil Brown told the club's official website: "It's great news that we've managed to bring Lee to the football club, I'm sure he can make a good impression.
"He obviously did very well for the club when he was here originally, and hopefully he can have more success in front of goal as he did then.
"Lee hasn't played much first-team football so far this season but did well during two loan spells in League 1 last season.
"We've got some very important games coming up and I felt it was key that we added another striker to our ranks."