The game was closely fought and only a winning strike from substitute Jemal Johnson, who was on-loan at Darlington two years ago, separated the two sides.
The visitors could have taken the lead after only five minutes. Good work from captain Keith Andrews saw the Dons threaten the Darlington goal and when the ball fell to Mark Wright inside the area, he looked certain to score until a total mis-kick allowed the Darlington defence to clear.
In the 12th minute Wright fired wide with a shot from the edge of the area.
The hosts began to get on top and Julian Joachim fired over the bar in the 13th minute and then defender Ian Miller headed over the bar in the 20th minute.
The Dons came back, and in the 33rd minute Dean Lewington connected with a deep cross from Lloyd Dyer with a header that flew inches over the bar.
Darlington began to take control in the second half and in the 49th minute Dons' keeper Willy Gueret failed to clear a long kick from Darlington keeper David Stockdale but his defence helped him out and the danger was cleared.
A minute later Darlington striker Pawel Abbott struck a post with a close-range shot and then in the 51st minute another effort from Abbott was well-saved by Gueret.
With a big crowd cheering them on Darlington almost took the lead in the 63rd minute when Rob Purdie had a shot saved and the loose ball fell to Abbott who somehow missed the target from 12 yards out.
In a rare second-half break forward substitute Jude Stirling crossed from the right in the 84th minute and fellow substitute Johnson fired in the winning goal from a narrow angle at the far post.