Winger Mark Bentley helped himself to two goals at Priestfield and although Alan Pouton pulled a goal back for Gillingham four minutes from time, Southend held firm and kept their considerable momentum going.
It came as no surprise that Southend started the game full of confidence and Mitchell Cole shot wide under pressure from Richard Rose in the opening 60 seconds before Wayne Gray's header from a Kevin Maher corner was well caught by Gills keeper Jason Brown.
Southend keeper Darryl Flahavan then pulled off an even more impressive save on 32 minutes, tipping over a powerful header from Andrew Crofts.
Gillingham were guilty of missing an absolute sitter in first half injury time.
Michael Flynn's long pass put Matt Jarvis through and he squared to an unmarked Neil Harris who somehow chipped wide when left with a four-yard tap in.
Southend made Gillingham pay for that miss with the opening goal on 56 minutes. Adam Barrett's free-kick from the right was turned back in by Gray and Bentley slid in to poke the ball home.
A horror moment by Brown led to Southend's second. He raced out of his area and left himself totally exposed as he headed the ball straight to Bentley who accepted the invitation to shoot into an empty net from 25 yards.
Pouton, a Gillingham substitute, scored his first ever goal for the club in the 86th minute but, despite five minutes of injury time, it was too little, too late for the Kent side.
For Southend a second successful promotion is starting to become a realistic possibility.