Terry Brown had guided the Dons from the Ryman League Premier Division to npower League Two since taking the reins in 2007 but waved a tearful goodbye after defeat to Torquay on Tuesday. With Simon Bassey in caretaker charge the Dons collected their first win since the opening day as Moore struck in the 40th minute after Byron Harrison missed a penalty.
It was the Dons who made early inroads, as Luke Moore's centre found Rashid Yussuff, but his header flew wide of the far post.
AFC Wimbledon were rewarded with a 35th minute penalty after Danny Foster was adjudged to have handled Harrison's strike. Harrison himself stepped up but Cardiff loanee Elliot Parish, making his home debut, got down smartly to his left to repel the spot kick.
But the visitors made amends just five minutes later, as Sammy Moore unleashed a spectacular half-volley which crashed off the underside of the bar on its way past Parish.
In a second-half largely devoid of chances Gareth Ainsworth fired over the bar from a corner for the hosts but that was as close as they came.