The England midfielder's second goal in as many league matches set up consecutive top-flight victories for both the second time this term – and under new manager Ralph Hasenhuttl.
Lucas Digne put through his own net for Saints' second, as the St Mary's Stadium men shook off their midweek FA Cup loss to Championship side Derby.
Gylfi Sigurdsson's neat finish set up a fraught finale but Saints held on for a fully-merited victory.
Austrian boss Hasenhuttl sat Ward-Prowse down before the turn of the year and told the one-cap England star to "toughen up" to maximise his talents.
The fruits of that heart-to-heart and Hasenhuttl's high standards are clear: two Ward-Prowse goals and two league wins, the 2-1 victory at Leicester and now this hard-fought triumph over the Toffees.
A fifth league win of a testing campaign now sends Saints into crucial clashes against Crystal Palace, Burnley and Cardiff in buoyant mood, intent on pulling further clear of the drop zone.
Hasenhuttl's Southampton transformation took another step forward here, in victory over an outfit hopeful of a top-eight finish.
Saints were rudderless under Mark Hughes – but Hasenhuttl has imbued shape, purpose and work-rate.
From the off, Everton's listlessness matched Southampton's inability to finish.
Danny Ings met Ward-Prowse's corner with a header to test Jordan Pickford, one the England goalkeeper palmed clear.
Jan Bednarek's chip over the top begged for a finish but Ings blasted straight at Pickford.
Ings and Pierre-Emile Hojbjerg linked up well to Nathan Redmond free next, but his low drive shaved the wrong side of the upright.
Ward-Prowse failed to control Hojbjerg's smart ball into the area as Saints pressed again, before Andre Gomes unwittingly played onto his own post in the act of robbing a prowling Ings.
Saints' frustrations at turning around without a goal were compounded by Everton starting the stronger after the interval.
But then out of nothing Ward-Prowse produced the thunderbolt strike that opened the scoring.
The 24-year-old's rising drive arced away from a helpless Pickford to settle Saints' nerves, briefly hotting up this often low-key affair.
Another fine Hojbjerg through-ball – a regular ploy to split Everton's centre-backs – sent Redmond haring clear. But before Redmond could even think of applying a finish himself, Digne flicked the ball past a stunned Pickford.
Everton attempted a rally but to little or no effect, leaving boss Marco Silva doubtless displeased with such a limp showing.
Saints kept on pressing in contrast, with the excellent Jack Stephens heading just wide from a corner.
Although Sigurdsson side-footed home late on for a well-taken Everton goal, the effort remained in vain as Saints swiped all three precious points.