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Manager Dave Anderson admitted he was "immensely proud" of his players and got the reaction he was looking for after last week's woeful 3-0 league defeat to Billercay Town.
He said: "When you win games like that you always think they are great games. As a cup tie I thought it was exciting.
"We rode our luck a little bit but so did they.
"To beat a Conference side with six or seven players out is something that myself and my players should be immensely proud of."
After a cagey first 10 minutes spell it was Wimbledon who created the afternoon's first clear cut opening after the lively Wes Daly and Steve Butler combined to set up former Aldershot striker Roscoe D'Sane in the box but his low angled shot was well saved by keeper Nikki Bull.
Then after a uneventful 15 minutes the game burst into life on 27 minutes when Aldershot's Louie Soares - older brother of Crystal Palace midfielder Tom - combined with Ryan Scott down the right flank to set up a chance for the Shots' impressive right-back Curtis Osano but he shot wide with only Little to beat.
For the remainder of the first half Aldershot slowly turned the screw on the visitors with John Grant and Osano again both going close to opening the scoring.
And it was no surprise just on the stroke of half time when great work from Aldershot's Kirk Hudson set up Grant whose powerful eight yard drive beat Little to put the Conference side a goal up.
The Dons were fortunate to go two down before the break after Osano and Hudson both came close to doubling the home side's advantage in first half stoppage time.
An Anthony Howard goal saving block from Ryan Williams's goal bound drive and a vital Little save from Hudson's low shot inside the first five minutes of the restart prevented AFC Wimbledon from going further behind The spirits of the Wimbledon's travelling support was lifted on 52 minutes when Butler's goal bound header from Lewis Cook's corner was cleared off the line and Fitzgerald's follow up was somehow saved by Bull.
Aldershot should have doubled their lead on 54 minutes after Grant's low effort after being put clean through was again well saved by Little and Williams' follow up was somehow blocked by Simon Sweeney.
Then on the hour mark Chris Gell blasted the Dons back into the cup tie with a stunning 20 strike that flew past Bull to put Wimbledon back on level terms.
And just as the travelling support finished celebrating they were forced back into raptures after D'Sane's mazy run down the right ended in his shot being parried by Bull only for Fitzgerald to slot home into an empty net to put Wimbledon 2-1 up.
The remaining 25 minutes should have been renamed the Andy Little show with the keeper making a string of fine saves from Grant, Scott and Harding to secure AFC Wimbledon's passage into the next round.
With thanks to the Wimbledon Guardian.Match report by Sam Mokbel.