Hayles struck midway through the second half for the Lions' second goal having provided for Peter Sweeney's first of the season.
Danny Dichio made sure of the win, the Lions' biggest at home this season, in the 64th minute with a well-taken shot, just minutes after being denied by Luke McCormick.
Late substitute Ben May could have added a fourth for Millwall, but tripped over his own feet with the goal at his mercy after Hayles had squared for the striker.
But late mistakes aside, the result re-ignites the Lions' play-off hopes and leaves Plymouth hovering three points above the relegation places without an away win since November 6.
Millwall were dominant from the outset and should have gone one goal up in the second minute when midfielder Josh Simpson twisted his way through the Plymouth defence before passing to Hayles.
But an unmarked Hayles could only blast the ball over the bar from just outside the six-yard box.
But the striker made up for his blunder in the 56th minute when he latched on to Dichio's through-ball then beat Peter Gilbert to fire in from 15 yards for Millwall's second.
He also had a hand in the home side's opening goal, in the 15th minute, when he beat the offside trap to put through for Dichio.
Dichio missed his cue, but Sweeney was on hand to collect the loose ball and tap in from four yards for his first goal of the season.
Plymouth looked dangerous on the break and former Lion Scott Taylor came close to levelling the scores in the 21st minute, but his 18-yard shot was kept out by Andy Marshall's finger-tip save.
Four minutes before the break Plymouth were awarded a free-kick just outside the area but Akos Buzsaky's effort flew inches high of the crossbar.
Millwall had a strong penalty shout turned down a minute before half-time when Hayles appeared to have been held back in the area but referee Paul Melin refused to budge.
Bjarni Gudjonsson was lucky to be handed only a yellow card early in the second half after his elbow left Jody Morris with a nasty cut above his eye.