Hayles latched on to substitute Kevin Gallen's neat pass and bulldozed his way past goalkeeper Darryl Flahavan to register his 13th goal of the campaign.
Up until that moment, Argyle seemed set to be denied a penultimate home victory of their successful 2006-07 campaign by a superb display from Flahavan.
The keeper made six fantastic saves as the Pilgrims strived to turn their dominance into goals.
Flahavan was beaten as early as the sixth minute when Sylvan Ebanks-Blake was teed up for his eighth goal of the season by Peter Halmosi, who robbed Peter Clarke and drove a cross across the face of the goal for the striker to apply the final touch.
Clarke went from villain to hero midway through the first half when he rose to get the merest of touches to Steven Hammell's finely delivered curling right-wing free-kick.
Ebanks-Blake stole the show from Southend's much-vaunted striker Freddy Eastwood, who was watched by Wales manager John Toshack on his return after a back problem.
Apart from a brief spell after the equaliser, Southend were totally on the back foot.
Ebanks-Blake hit the post from a tight angle after bursting on to Akos Buzsaky's ball into the box, before the Hungarian playmaker then saw Flahavan turn a long-range shot round the post.
Hayles was the next to be denied by Flahavan, who spread himself to block the Argyle skipper before Buzsaky saw a 30-yard dipping free-kick hit the crossbar.
In the second half, he repeated the dose with a tremendous effort that Flahavan stretched full-length to turn aside and then laid on an opportunity for Paul Connolly who hit the side-netting.