Dale had taken the lead on the stroke of half time through Jack Stewart, but were left to rue missed opportunities as two quick fire second half goals ensured progression for the Magpies, who went through to the third round of the competition with a 2-1 win.
Andrew Hollins and Harry Pratt, who featured in Dale’s first round win over Altrincham, missed out through injury.
Academy goalkeeper Bradley Wade, who is just 15 years old, made his Youth Team debut after being handed a place in the starting eleven.
Conditions were difficult, as Storm Barney brought swirling gale force winds and driving rain to Meadow Lane.
Notts County started brightly and had the better of the ball in the opening exchanges.
They were the first to threaten the Dale goal, when they awarded a free-kick on the edge of the area after five minutes. Dominic Brownhill’s free-kick was deflected into the path of a team-mate, who saw his effort at the near post deflected behind for a corner ball, which was punched clear by Wade.
Three minutes later and the Magpies' McMillan sent a low ball across the face of goal. It was a dangerous ball into the area from the by-line, but Wade stuck out a foot to turn the delivery round the post.
Notts County continued to probe but Dale were resolute and limited the hosts' clear cut opportunities. Rochdale grew into the game and finished the half with a flurry.
On 29 minutes Tyler Berry sent an effort from distance narrowly wide of the upright, before goalkeeper Joe Searson-Smithard denied Jack Stewart, who had Dale’s best chance of the match so far on the half hour mark.
Jack Stewart twisted and turned inside the area before getting his shot away, but he was kept out by the legs of the ‘keeper.
A couple of minutes later and Dale tested again, this time from a set-piece which looked to have come straight from the training ground and left the goalkeeper stranded. After being played short, the ball was whipped into the area towards the back post, where Louis Coyne hit over the bar.
Momentum was with Rochdale and they opened the scoring in stoppage time as Stewart latched onto the end of a Brandon Smalley free-kick.
HT: NOTTS COUNTY 0-1 ROCHDALE
A minute after the re-start, Wade pulled of a wonderful one handed save to push a Notts County free-kick from 20-yards over the bar.
Despite a bright start by the Magpies, Rochdale went on to create the better of the chances before Notts County equalised.
In the 69th minute Berry got to the byline before sending a dangerous ball across the face of goal. The unmarked Stewart, who had matched his run, rose in the air, attempting to make a connection, but the delivery was just too high and the chance was squandered.
Two minutes later and the home side drew level through Montel Gibson, who lobbed the goalkeeper from the edge of the area.
Immediately after the goal, Dale’s Berry had an effort beaten away by Searson-Smithard, but it was the Magpies who went on to take the lead as they netted their second goal in the space of four minutes.
McMillan’s corner swirled horribly in the wind and curled towards the back-post where it was headed into the netted by a Rochdale player.
Jordan Prescott replaced Berry in the 80th minute and he came agonisingly close to netting a last gasp equaliser, which would have taken the game to extra time.
Smalley was firstly denied by Searson-Smithard, who sent the ball into the path of Prescott. He rounded the grounded ‘keeper but while under pressure from several Notts County players, he was unable to get a shot away, allowing the goalkeeper to get a touch. He attempted a second effort, which was cleared off the line by Jordon Richards.
FT: Notts County 2-1 Rochdale
Dale XI: Wade, Mata, Coyne, Evans, Schorah, Kisimba, Lenehan, Smalley, Berry, Stewart, Gillam. Subs: Piggott, Prescott, Chea, Price.