Bailey bagged his 11th goal of the season from 12 yards when he latched on to a Tommy Black cross from the right and beat Dean Brill at his near post after 37 minutes.
And Walker wrapped up the points in stoppage time when Brill kicked Matthew Spring's back pass out the Blues striker and he netted from 12 yards.
The win signalled the end to a run of nine league matches without a victory over the Hatters and left Luton still in the relegation zone following the deduction of ten points for going into administration.
Southend should have taken the lead in the 13th minute, but Richard Jackson cleared Charlie Mulgrew's effort off the line, before the right-back combined with Brill to block Hal Robson-Kanu's follow-up and Brill then saved Simon Francis' final attempt on goal.
In the second half Brill saved Robson-Kanu's point-blank header and then saw Mark Gower blast into the sidenetting with just the Hatters keeper to beat.
The hosts had several other wayward attempts at goal in a game that will not live long in the memory.
But after the match Shrimpers manager Steve Tilson was not complaining as the victory lifted his side into the play-off places ahead of their Roots Hall encounter with Nottingham Forest on Tuesday.
Luton's best chances saw David Bell head tamely at Darryl Flahavan in the opening minutes when he should have done better, before the Southend keeper saved his curling shot in the second half.