A John Rooney double condemned Whites to a second consecutive league defeat.
Last season’s National League Player of the Year, who joined Stockport in the summer from Barrow, slammed home a second half penalty, before slotting in his second and County’s third late on.
Substitute Alex Reid had earlier doubled the home side’s lead as Athletic were unable to build on a first half clean sheet.
Andy Hessenthaler’s men, including centre-back and academy youngster Will Moses making his National League debut, defended resolutely throughout the opening 45 minutes and nearly stunned the home side when Steve Rigg slid and narrowly missed Ade Azeez’ vicious cross into the Hatters’ area.
It took the hosts until just before the break to have their first meaningful effort on goal as Connor Jennings mis-kicked twice within the space of a couple of minutes.
The home side made their breakthrough when another Dover debutant, goalkeeper Josh Bexon, upended Reid in the area, with Rooney making no mistake from 12 yards as he sent Athletic’s stopper the wrong way.
Reid volleyed over from the edge of the box, but the attacker was more precise with his next opportunity.
The striker converted Richie Bennett’s pass, and despite protestations from Dover for a foul on Will De Havilland in the build up, the goal stood, leaving Hessenthaler’s side with the challenge of scoring at least two goals.
That task proved insurmountable for Whites and though Rigg went close with a close-range header, it was Stockport who put the game beyond doubt at the end when Rooney fired Sam Minihan’s lay-off into the bottom corner.
Earlier, boss Hessenthaler made three changes to the side that started the 4-1 against Bromley on Tuesday night, with Bexon, Moses and Bilel Hinchiri replacing Yusuf Mersin, TJ Bramble and the injured Harry Ransom.
Dover are back in league action on Tuesday 13th October when they host Aldershot Town, kick off 7:45 pm.
Two second half goals from Inih Effiong saw Whites bounce back from midweek defeat with a victory at 10-man Stockport on Saturday.
After Paul Turnbull had been sent off shortly before half-time for a dangerous foul on Effiong, Athletic’s striker bagged his 12th of the season soon after the break.
And the striker had his 13th of the campaign ten minutes before the end, volleying home after his initial shot was saved by home keeper Ben Hinchcliffe to give Andy Hessenthaler’s men a second win in three league matches.
Earlier, Michael Woods blazed over from the edge of the box early on and Liam McAlinden slashed wide from a similar position at the other end.
Danny Lloyd then intercepted Jack Munns’ loose ball, running half the length of the pitch and sending a teasing cross that just evaded teammate McAlinden.
Oscar Gobern then headed Munns’ corner on target, only for Turnbull to nod off the goalline.
However, County captain Turnbull’s afternoon would take a turn for the worse five minutes before the break.
The defender went clattering into Inih Effiong as the two opposing players challenged for the ball, with Turnbull given his marching orders by Simon Mather after Athletic’s striker was left in a heap on the floor following the dangerous tackle.
Whites were able to make the breakthrough four minutes after the restart.
Jai Reason intercepted Ash Palmer’s miscontrol to then find Effiong, who after taking a touch, slammed his 12th goal of the season into the bottom corner.
Kevin Lokko’s heart was almost in his mouth when he inadvertently diverted Adam Thomas’ cross onto the inside of his own post, with substitute Bobby-Joe Taylor on hand to clear the danger.
Ashley Maynard-Brewer was then called into action for the first time since signing on loan from Charlton Athletic earlier in the week.
The visiting keeper dived to keep out Lloyd’s fizzing shot at his near post.
At the other end Effiong made no mistake with his second goal of the game.
The striker outmuscled his marker to latch onto Steven Rigg’s flick and though home stopper Ben Hinchcliffe saved his first effort, Effiong was on hand to volley the rebound into the bottom corner, his 13th strike of the campaign.
Effiong nearly had a first hat-trick for Dover after sprinting clear, only to fire into the side netting after Hinchliffe had come sprinting out of his goal.
Earlier, boss Hessenthaler made three changes to the side that started the 4-2 loss at Halifax on Tuesday evening. Aaron Simpson and Munns replaced the ill Shadrach Ogie and Taylor, who started on the bench.
Ashley Maynard-Brewer, signed on loan from Charlton Athletic earlier in the week, was also handed a debut, with other recent loan signing Dominic Poleon named as a substitute.
Whites next host Barrow on Tuesday 4th February, kick-off 7:45 pm.
DOVER ATHLETIC REACTION
STOCKPORT COUNTY REACTION