Miller's left-footed strike gave the south coast visitors a first half lead with a sharp finish on 17 minutes.
The 28-year-old forward, who has attracted interest from Football League clubs this season, was also involved in Dover's second as Ricky Modeste headed home moments after Miller had hit the post.
And he capped a man of the match display on 83 minutes as he smashed home a penalty he won.
The visitors were then awarded a second penalty in injury time which substitute Ross Lafayette dispatched.
The 18th loss of the season leaves Guiseley within the clutches of the club's fighting relegation while Dover strengthened their hopes of finishing in the play-off places.
Lions boss Adam Lockwood had swerved the temptation to throw returning Leeds United loanee Alex Purvis back into his starting line-up as he maintained the same team that drew 1-1 at Gateshead.
Purvis, who joined on Non League deadline day on Thursday, had to settle for a place on the bench, instead, while fellow Leeds loan recruit Michael Taylor was left out altogether.
The visitors were boosted by the return of National League topscorer Miller from a two-game suspension.
After a open start, Miller gave the promotion-hunting visitors a 17th-minute lead.
From a deep free-kick, the ball dropped at the feet of the striker and he lashed home his 33rd goal of the campaign into the bottom corner.
Guiseley came close to levelling inside two minutes as Jake Cassidy headed wide from a corner.
But the wave of play flowed for the away side and Miller's trickery and wand of a left-foot crafted a number of opportunities.
The 28-year-old, who was the subject of a six-figure bid from Peterborough in January, set Moses Emmanuel up for a poor header over before the winger smashed another chance high and wide.
Guiseley improved in the final minutes of the first half but Kevan Hurst was unable to test Mitch Walker in the Dover goal from a 25-yard free-kick. When the Lions midfielder did draw a save out of Walker, the away stopper was equal to it low to his right.
Miller showed his quality again on the stroke of half-time with a vicious shot from distance that flashed narrowly wide.
Dover started on the front foot after the break, too, and Emmanuel found the side netting before James Hurst curled over from neat work by Miller.
Purver made his introduction on 58 minutes in place of former Leeds midfielder Simon Walton and drilled an effort wide with the outside of his right boot with his first involvement.
Dover's second arrived soon after a surprising miss from the away side's main man Miller. A long punt left Maxted in no man's land and bounced kindly for the striker, whose dink towards goal bounced onto to the post.
Emmanuel recycled the ball and his deep cross found Modeste waiting at the back post to nod in.
Miller sealed a comprehensive win for the visitors on 83 minutes as he rolled inside from the right-flank and tumbled under Danny Lowe's challenge.
The striker made no mistake from the ensuing penalty with an emphatic finish into the left-hand top corner.
Miller was not given the chance to seal a fourth hat-trick of the season as he was subbed two minutes after the penalty.
With the main man off the field, Lafayette took over penalty duties and sent Maxted the wrong way after Dover were awarded a second spot-kick of the final 10 minutes.
Guiseley: Maxted, Brown, Lowe, Lawlor, Hurst (Asamoah 73), Hatfield, Palmer (Rankine 73), Preston, Williams, Walton (Purver 58), Cassidy
Subs: Boyes, Wesolowski, .
Dover: Walker, Essam, Orlu, Modeste, Miller (Pinnock 85) , Fazackerley, Grimes, Sterling, Emmanuel (Lafayette 70), Healy, Hurst (Kinnear 85)
Subs: Skapetis, Caton,