Despite the sides' league positions, it was a scrappy start to the first half, but Brentford will not complain since it eventually brought them a scrappy opening goal.
Adam Barrett was caught in possession in his own half on 23 minutes by Ricky Newman, who played in Isaiah Rankin.
His shot was weak but it beat visiting keeper Darryl Flahavan and despairing defender Duncan Jupp only managed to bundle it over his own line.
The home side controlled the game from there on, and with Southend pinned in their own box on 32 minutes, Kevin O'Connor took a throw to the near post and a looping Sam Sodje header forced a save from Flahavan.
From the resulting corner, the same man got up at the near post and came even closer as a more powerful header was tipped onto the bar by the Shrimpers keeper.
Although two follow-up shots by Sam Tillen were blocked by Barrett, the Bees soon found the net again, as another corner swung into the near post was this time met by Marcus Gayle, who made it 2-0.
The visitors did manage to finish the first half the brighter side however, with Mark Bentley scooping a gilt-edged chance over the bar from five yards after a Mark Gower cross found him free at the back post on 40 minutes.
They had their best chances of the second half during the last half hour, with Luke Guttridge having a goal disallowed and Freddy Eastwood hitting the post with 15 minutes left.
However, the Bees nearly put the icing on the cake when Darren Pratley saw his 25-yard free-kick crash against the crossbar on 79 minutes.
They continued to hold on to possession late in the game, and claimed the three points mainly thanks to a great defensive performance.