Rowett, previously assistant manager, took temporary charge alongside Kevin Poole after Paul Peschisolido was sacked in mid-March on the back of a dire 14-match run without victory.
He broke that unwanted sequence just 10 days later before going on to win three and draw two of the club's final 10 league games to secure Football League survival, albeit losing five including a 7-1 mauling at Bristol Rovers.
Burton chairman Ben Robinson told the club's official website: "I'm very pleased to be able to announce Gary Rowett as our new manager.
"Gary took over at a difficult time for the club after a long string of poor results and he has been able to achieve safety in the Football League, which was the primary aim.
"We now look forward to a summer where I am sure the necessary changes will be made as we plan for the upcoming 2012/13 season.
"I have been impressed by Gary both during his time as assistant and caretaker manager and I have every faith he will prove to be a success as the manager of Burton Albion on a full-time basis."
Rowett, a former defender, played 47 games for the Brewers before returning to the club as assistant manager to Peschisolido in 2009.