Beattie, 35, succeeds Leam Richardson, who left last month to become Paul Cook's assistant at Chesterfield.
The former Southampton and Everton forward, who won five international caps, has been player-coach at the Crown Ground since November.
Stanley finished the season in 18th position in the table, three points clear of the relegation zone.
The club announced Beattie's appointment after holding interviews with prospective candidates this week.
Their former manager John Coleman, who was sacked by Rochdale in January, had also been linked with the post.
Coleman spent 12 years at Accrington, taking them back into the Football League and reaching the League Two play-offs in 2011, before leaving to join Dale in January 2012.
Managing director Rob Heys told BBC Radio Lancashire on Friday: "We want someone who's going to keep the team spirit going, someone who's going to work very hard with a limited budget, and someone who fits in with the general feel of Accrington Stanley,"