Scott, who had been without a job since leaving Rotherham in March last year, takes charge with the Shots two points above the League Two relegation zone.
He will be assisted by Terry Bullivant and the duo have signed deals until the end of the 2013-14 season.
A club statement said: "Having drawn up a shortlist of credible candidates since the departure of Dean Holdsworth, the board of directors felt that the experienced team of Andy and Terry offered the football club a real opportunity of making progress in the immediate and longer term."
Scott says he is confident of the club retaining their Football League status this season.
Shots chief executive Andrew Mills said: "The deal will be until 2014, even if the club go down.
"We needed a credible management team."