Two goals in second-half stoppage time snatched all three points for Derry City as they rallied from 2-0 down to beat Waterford United 4-2 at the Ryan McBride Brandywell Stadium.
Waterford took the lead through Jorgen Voilas in the first half and a Tommy Lonergan penalty increased their advantage early in the second period.
Duffy inspired the comeback, scoring twice to level the game before a thumping header from Dipo Akinyemi completed the turnaround.
The Derry skipper then sealed his hat-trick as well as the victory with a spot kick of his own in the closing stages.
Candystripes fight back to win late
With the week two fixture away at Dundalk being reversed to allow for work to continue at Oriel Park, four home games to start the campaign seemed like the perfect launching pad for a Derry City title charge.
Nevertheless, Tiernan Lynch's side came into Friday's game with just four points through three matches and off the back of their first loss of the season to Bohemians last Friday night.
The Candystripes are yet to score first in a game this season and that trend continued when Voilas capitalised on a Derry defensive mix-up to give Waterford the lead.
Things went from bad to worse for the Foylesiders when Adam O'Reilly brought Lonergan down in the area shortly after the interval.
Interestingly, with Padraig Amond having missed from 12 yards last time out for the Blues, it was Lonergan himself who stepped up and slotted a well-placed penalty past Eddie Beach in the City net.
On the same weekend as when they won this fixture this time last year, Waterford again had a firm grip on all three points, but a stooping header from Duffy on 58 minutes gave the home side a flicker.
Then, in the 75th minute, the 2025 PFAI Men's Player of the Year displayed sheer class to control a Henry Rylah cross on his chest before rifling a volley into the roof of the net to level the game.
Derry destroyed their Munster counterparts during their most recent trip to the Brandywell with a 7-2 rout; however, this time, proceedings were much more dramatic.
Things could have ended much differently as Conor Carty almost restored Waterford's lead with 10 minutes remaining, but his effort rattled the frame of Derry's goal.
As the clock entered the red, Duffy's free-kick was met by an unstoppable Akinyemi header to complete the comeback, with the substitute deservedly getting on the scoresheet.
Duffy made no mistake in securing all three points and rounded off his hat-trick with a penalty.
Derry move up to second ahead of a trip to face the champions Shamrock Rovers at Tallaght Stadium next Friday night, while Waterford remain ninth at this early juncture.